Has/tak stuff: cut and keep the back. Any toys purchased at over 100$: Keep box, inserts intact as they are.
If I had the packaging for each transformer, I would just save the outside of the box and throw away the inside packing.
I have kept two boxes - my G1 Jetfire and my Wingblade Animated Prime. Everything else has gone in the recycling.
I throw away all but G1 (of course), Botcon/TFCC (of course), Masterpiece, and the odd rare figure box. But mostly they go into the recycling bin. It's not that I wouldn't like to have a set of pristine boxes, it's just a space issue.
I used to keep everything when I started collecting which I guess was cool because I still have all my alternator boxes now. But I quickly found out how fast this stuff takes up storage space, and I only keep boxes for imports, hasbro masterpieces, and us exclusives now.
Unless it's something like third party of the old Book Style reissues the packages go into the trash.
I even threw away my Book Style boxes. I did however keep the front flap with the pretty picture book attached to it.
I just tossed a PILE of newer boxes - Classics, etc. I keep the G1 boxes, and the MPs - but this other stuff just took up too much room. I had boxes OF boxes - ugh. They all got trashed - no regrets.
I try and keep cardbacks and boxes, but if they rip or tear I just toss them. Not a big deal. I do keep all 3rd party stuff though.
Kept MP Skywarp, Unicron, and my Alternators boxes for storage. The rest are just packaging, and I'm no -in-box collector.
I usually toss boxes and cardbacks/bubbles. There are definitely some exceptions, though. If I really like the artwork or the toys were a present then I'll usually keep at least cardbacks. I still have the cardbacks for the first wave of Classics and TFTM Deluxes because they were gifts from my wife.
I keep all the cards (but not the bubbles) and boxes. i have them boxed up ironically. I have gone back at certain times and sold some of my collection and they have really come in handy for resale. i actually keep every box for everything i own if possible. they come in handy when i have moved to be able to re-box things like laptops, surround sound etc. much easier to stack in moving trucks. and also for resale value. My house got broken into a few months back and they took my xbox 360, wii, laptop, PS3and my wife's jewelry. while we haven't gotten most of it back, the boxes did have all the serial numbers on them so I used that to give to the police and they found my PS3 and a few other things. i had already bought a new PS3 before they found it so when i sold it, it had everything that it came with and i got more money for it. same with a firestudio recording interface. the buyer paid more because i had everything including the box. So in my opinion, boxes become very valuable for many reasons if you have the room to keep them!
I toss most of everything anymore I used to keep the backs but I didint see the point after awhile. I do keep boxes for stuff not TF outta Japan though because those are just too damned awesome to toss
I keep all G1/MP/Takara/3rd party boxes and have saved some of the larger A/E/C boxes over the years just to store figures in.
I keep all the boxes for MP, 3rd party and I keep the back cards for CHUGS. I file the instruction booklets in my file cabinet.
I do keep deluxe boxes by putting some tape on the ripped parts but I think I might not do that anymore and only keep the MP and third party boxes (which I've already done with my MP Megatron box with the accesories staying inside)