I remember seeing a "Favourite Character from each series" thread a while back, and wondered the same in regards to episodes.

Anyway for me it's probably:

G1: Call of the Primitives - Just super well animated and fun. Also kind of terrifying to watch as literally every main character dies at some point through the episode.
BW: Code of Hero - You expected anything else?
BM: The Catalyst - Probably. It's been ages since I've watched Beast Machines, but I've always liked that episode specifically for the Thrust reveal. It would probably change if I rewatched it at some point.
RID: Attack from Outer Space - I love Movor.
Armada: Tie between Cramp and Mortal Combat - Both are straight up well made episodes.
Energon: The one where Demolishor dies.
Cybertron: Scourge - There are better eps, I think. But this one was especially fun to me. Same deal with Beast Machnies, as I haven't watched Cybertron in ages.
Animated: Tie between Thrill of the Hunt and Transwarped probably. Decepticon Air was also great.
Prime: Thirst - It was refreshing to have an episode that was fun, while also focusing on probably the two best characters in the show.
RID2015: Bumblebee's Night Off - Solidified Bumblebee as a favourite of mine. Same with Bisk.

 

The other series had good episodes, but not one I would watch over and over.... except maybe this one:

TFA Five Servos of Doom

 

At that episode when the band was playing, everyone at the concert was doing the "Rock on" hand gesture wrong and I got so damn pissed.  

Anyways, here are my fave episodes from each episode
BW: Code of Hero and Nemesis Part I and Part II
BM: Techno-Organic War Part I and Part II
Prime: Deadlock (C'mon the final episode was awesome)
RiD The Decepticon Islands episodes, Bumblebee's Night Out and Portals
Rescue Bots: Today and Forever
TFA: Theres a lot...my favorites are the Megatron Rising Episodes, Five Servos of Doom, Along Came a Spider, the Human Error episodes, and the Endgame episodes

I haven't watched much of the Unicron Trilogy and RiD 2001

 

G1: Starscreams Ghost
Thats the only series i watched LOL my favorite live action movie is the first one... thats all.

 

You've only watched G1?

 

All episodes of G1 are comedy gold and perfect.

Need to watch Beast Wars. I like all the episodes in BWII where BB and Starscream do all kinds of fun gay shenanigans together.

Love Secret Weapon: D-5 from RID cause Midnight Express is best waifu.

Rebellion, Mars and Mortal Combat are my choices for fav Armada episodes.

My memory of everything else is too hazy to pick out favourites. I liked most episodes of Animated  

 

Yup

 

Then what do you do???   

 

Hehehe i just watch G1 and watch em' again! All i hear is bad things from stuff like Armada, ect, and ive tried Beast wars and cant stand it, so i might try Animated.

 

G1: Fight or Flee
Headmasters: Ultra Magnus Dies!!
Super God Masterforce:
Victory: Ginrai Dies!!!
BW: Code of Hero
RID:
Armada: Cramp
Energon: Farewell Inferno
Cybertron:
Animated:
Prime: Darkest Hour
RID15: Pretzel Logic

I don't really have a favorite from SGM, RID, Cybertron, or Animated. I never watched Beast Machines or the Japanese BW shows.

 

G1: Rebirth
Animated: Transwarped
Prime: Darkmount, NV. Scattered. Prey

 

G1: More than meets the eye parts 1, 2 and 3. Closely followed by Dark Awakening.

Beast Wars: The name escapes me. Optimal Situation I think where Primal takes the Matrix from Optimus Prime.

RID 2000: The first episode with Scourge.

Prime: New Recruit

Animated: the one where Starscream keeps dying

RID 2015: first episode with Starscream

Combiner Wars: Episode 4 which introduces Megatron

 

Let's see...
Armada-Cramp, Mortal Combat, Linkup
Cybertron-All of them, but the main ones are United, Optimus, Guardian, and Unfinished
Animated-The Endgame episodes
Those would have to be my favorites.  

 

It has been so long since I watched most of these series, I don't particularly put my thoughts towards which episodes are my favorite, and have totally forgotten all the episode titles, so I'll try my best.

G1: Got more than a few here, and I can't really decide:

The episode with the big game hunter is great. It starts with him hunting a Russian jet and just gets sillier from there.

The Seaspray episode. Camp does not get any better.

The one where Cyclonus admits Galvatron to the Asylum Planet. I'm one of those weirdos whose favorite season is the 3rd one. I like Galvatron way more than Megatron because his motivation is because he is insane instead of just doing stuff because it is evil. I mean, being under thrall to an elder god type monster when that monster gets destroyed cannot leave a person in a stable mental state. This episode really shows what sets Galvatron apart from Megatron.

The episode where Rodimus Prime must mediate peace talks between two planets who are being manipulated into war by the Quintessons. I appreciate that this episode does not have a clean resolution. I prefer Rodimus to Optimus because he does not always succeed.

BW: Code of Hero, for obvious reasons. I also like the episodes dealing with the Vok. I really like having a very alien faction throwing a wrench in the works. I just wish that the Vok had more of a resolution in the story.

BM: Really like the series finale. I found that the BW finale felt rushed, and this one feels way more solid.

RiD2001: Probably the Fish Test episode or the one where Kelly is in Vegas and the Autobots have to stop a dam from being destroyed. Sky-Byte is one of my favorite characters, and Kelly is a really good running joke.

Armada: Everything after the return to Cybertron dealing with the formation of the Armada and the fight against Unicron. I can't name any individual episodes because I binged this series and all of the episodes tend to run together.

Energon: I think towards the beginning of the series Optimus faces off against the resurrected Megatron for the first time and had a pretty cool looking anime fight where the scenery gets destroyed everytime they clash. I don't know. Maybe. There aren't really any high points in Energon.

Cybertron: The final episode. I love epilogue episodes to series and this was a great send-off. I also like the part of the final fight where Optimus gets Vector Prime's sword.

Animated: Season 2 finale and the beginning of season 3. What happened to Sari is one of my favorite twists.

Prime: Season 2 finale and the beginning of season 3 (again). I really like how dire things get. Granted, everything is fine by the end if these episodes and the potentially interesting idea that Smokescreen becoming a Prime is completely dropped, but it was a fun arc regardless.

Rescue Bots: I am currently trying to catch up on this series, so I only have knowledge of the first two seasons. Anytime Morocco shows up is pretty fun, so I'll go with the time travel episodes.

RiD: While I like this series, none of the episodes particularly stand out to me. I like Pretzel Logic, but that may just be on my mind since I saw it recently.

I have also seen Headmasters and Combiner Wars. I thought Headmasters was going to be more G1 goodness, but instead of telling goofy or interesting one-offs, it spent most of its time telling a slightly boring on-going story. I guess when they destroyed Cybertron and Mars was pretty shocking, so I'll put those episodes as my favorite.

As for Combiner Wars, I view it more as a movie split up into parts, so I can't really pick out my favorite episode. Not that I have a favorite episode of that show. Honestly, it was pretty bad, with the only highlight being a very interesting interpritation of Megatron. I mean, CW Windblade is just terrible, and dumb video game boss Starscream was even worse. I actually really like IDW and RiD Windblade. Most complaints about her is either displeasure at her being a fan create-a-character/a new G1 Character/her being made to appeal to fans and some misplaced Chromia hate. But CW Windblade is just an angry murderer with no appeal at all.

 

G1: Dark Awakening. A really dark episode with a surprisingly sad ending. It's one of the few episodes where I genuinely found Rodimus likable, and the reanimate, partially mind-controlled Optimus Prime was extremely well-executed. "They made me a weapon to destroy the very ones I loved in life..." makes me tear up every time.
Beast Wars: Code of Hero. I couldn't do justice explaining this episode. Just an all around awesome episode focusing on the redemption and demise of the best character Beast Wars gave us.
(Didn't see much of Beast Machines, RID2001, or Energon, haven't watched Armada or Cybertron in years...)
Live-Action Movies: I thought the first one was genuinely good. It built up its story pretty well, and even though you had to sit through human-dominated scenes of varying qualities between "ugh" and "okay", the whole movie steps up several levels of awesome once Bumblebee reveals his robot form and the rest of the Autobots enter the scene. They give some character to each of the Autobots, and it gave us an extremely memorable final battle.
Animated: Ooh... a tough one... I haven't watched this series in a while... I'm gonna go with Transform and Roll Out Parts 1 - 3, for nostalgic purposes. It was a great start to the series, yes, but I'll always remember it as the first piece of Transformers fiction I ever watched.
Prime: Too many really good episodes... I'm gonna go with the One Shall Stand/One Shall Fall/Orion Pax arc. They do a great job building up Unicron throughout these episodes, they have memorable exchanges and battles in these episodes, and even the subtle moments, like Megatron nodding just before Optimus reveals the existence of the Matrix. I know a lot of people were disappointed that the Autobots successfully restored Optimus Prime's memories, but I felt like it was an extremely satisfying conclusion after seeing the lengths the Autobots go through for the sake of their leader. I could fanboy for hours about how these episodes sum up everything I love about Transformers, but I'll cut myself off here.
Robots in Disguise (2015): Pretzel Logic. Robots in Disguise has had its ups and downs, and I'd still consider it an imperfect series, but I do feel it's gradually getting better, with the Scavengers/Starscream arc highlighting that for me. So, we get an episode focused on Grimlock trying to learn to control his eagerness to fight and his destructive capabilities. How is he taught this? He meets a monk, and they bond over making pretzels. It's silly, but in all the right ways. not to mention Brother Gunther is such an enjoyably open and friendly character. We are also introduced to my favorite of the Weaponizer Mini-Cons with Tricerashot, and after Paralon and Scatterspike were almost the same character, personality-wise, Thermidor was a nice change with his pirate personality. Strongarm's and Sideswipe's little exchange was a nice bit of the show poking fun at its own characters, and the interactions between Grimlock and Gunther or Grimlock and Bumblebee really sell this episode to me.
Combiner Wars: Ohhh, boy... I can't remember the titles of any of this series' episodes, and the series just got worse as it went on... I dunno, the episode where Windblade and Optimus confront Megatron on some jungle planet while he's beating up the Constructicons. Megatron and Optimus were the best things about this series, and the episode delivers some interesting dialogue exchanges between them.

 

Sure, let's say go!

G1: Webworld
Headmasters: Ultra Magnus Dies!
Masterforce: Super Ginrai Gets Blown Away in the Desert!?
Victory: Showdown! The Fortress vs the Victory Unification
BW: The Agenda
BWII: The Black Lio Convoy
BWNeo: The Final Battle
Beast Machines: End of the Line
RID: Commandos
Armada (ugh): Past
Superlink: Resurrection! Galvatron
Cybertron: Family
Animated: Megatron Rising
Prime (ugh): Sick Mind
Rescue Bots: The Lost Bell
RID'15: Rumble in the Jungle


Some of those were pretty easy and just typed the series and episode as one line from memory. Others I had to use the Wiki to take a look and then made a choice. For two, I just chose ones that I probably wouldn't be enraged to be forced to watch again.

 

Ok.

G1: Hmmmmm....... I'd say "Starscream's Armada" Mostly because it introduced my favorite Combiner EVER and is also very whimsical.
Headmasters: "TERROR! The Six Shadows" Because, Sixshot. Also, I CANNOT UNDERSTAND WHY EVERYONE THINKS ULTRA MAGNUS'S DEATH WAS SO EMOTIONAL SERIOUSLY HE DIED IN AN IDIOTIC WAY and a STUPID way at that.
BW: "Code of Hero" or "Nemesis Part 1" Because DAMNIT WHY YOU GOTTA KILL DEPTHCHARGE AND DINOBOT
BM: "None" (I haven't seen the series yet)
RID: "Sky-byte saves the Day" It focuses on Sky-Byte and I loooove Sky-Byte.
Armada (yay): "Cramp". Definitely Cramp. I mean, Starscream had this ENTIRE story arc that mixes IDW Thundercracker with the Starscream individuals we all know and love, and OH. MY GOD. IS it ever amazing. And all that Story Arc came and ended here. I love it. I Love it. I LOVE it.
Energon (Booooo): Nope.
Cybertron (Ok, I actually like this one.): "Memory" or "Beginning"
Memory because I genuinely liked the plot and Beginning, because Beginning was a nice and fitting end to the entire series.
Live-Action: Live-Action technically does not count but I'll do it anyways.
I liked the 4th movie because it introduced so many good and new characters while giving the old ones some decent justice. Would've liked to see more out of the Wreckers, because DANG IT! WE ARE SUPPOSED TO HAVE TWINTWIST WITH TOPSPIN. But Overall, it's a fitting end to the older guys. Except Ratchet. Screw you for killing Ratchet Lockdown.
Animated: "SUV" Because SWINDLE!
Prime: Every. Episode. Ever I cannot decide. (Actually if i had to decide it would be Crossfire because come-on, Wheeljack and Dreadwing are B-A!
Crossfire is my favorite because It introduced/reintroduced two awesome characters and an amazing sub-plot of Wheeljack wanting revenge on Dreadwing for killing one of his Wrecker buddies. Also, the name drops!
RID (2015): "Worthy"
Combiner Wars (Ugh): "War of Giants" because Devastator, or Episode 4 i think, because Optimus vs. Megatron was the ONLY redeeming episode in that horrific series.

Is that it? wow.

*edited.

 

Wait. wat.

 

G1: three way tie between Call Of The Primitives/Webworld/The Ultimate Weapon

BW: Code Of Hero (But to avoid being cliche, I'll put down The Agenda Part 3 as a close 2nd.)

BM: Revelations Part 3

RID: The Fish Test

Armada: Cramp

Energon: Cybertron City (ie. The only decent Energon episode)

Cybertron: Fury

Animated: Five Servos Of Doom

Prime: One Shall Fall

RID 2015: Portals

 

Hmm. Other than G1 and Beast Wars, I don't think I have a favorite episode from any TF series. Even Beast Machines and Animated, both of which I like a lot, I don't think I could pull out a specific episode I like above all others.

G1: Five Faces of Darkness (if the '86 movie doesn't count as an episode), runner-up: The Rebirth

Beast Wars: the one where Ravage dies. "DECEPTICONS FOREVERRRR!!!" Honestly, I found his death far more moving than Dinobot's.

Animated: All of seasons 2 & 3. I honestly don't think I can narrow it down any further than that.

Everything else: ?? ??