As far as stuff you could've walked into a toystore and bought off the shelf/pegs? I figure Bumblejumper is right up there. Couldn't have been too many of those floating around. Legit Japanese dinocassettes will give your wallet a good beating, but I can't speak to their rarity. I see them for sale less often than Bumblejumpers, though.
I just thought of something else. The Energon Built to Rule stuff is actually very rare. It only got released here in Cincinnati, and I believe one or two other test markets and that's it. I remember not long after they came out, they were actually being sold for a lot of money online. It was pretty hilarious.
It has to actually exist to be considered rare. Another contender: G2 Bullet Bike. I don't think I've ever SEEN one of these guys. Same with the European Aquaspeeders.
As far as mass retail releases, I believe the rarest might be Energon Ultra Magnus, Treadbolt and Rapid Run. The wiki says there were only 10,000 produced of each one, so in terms of actual production numbers for figures that weren't intended as contest prizes or con exclusives, they might be the winners. Despite the fact they shelfwarmed in the rest of the world.
Well, there are a couple of toys that are one-of-a-kind. This G1/ Alternators Jazz comes to mind (third one down): Jazz (G1)/toys - Transformers Wiki
Who says it doesn't exist? Maybe you just can't find him... Because he's, ya know, Mirage, and.. *cough*
My guesses: G1 guys like Skyshadow and Minerva Animated Thundercracker US Animated Blackout HFTD Sideways sneak attack 4-pack HFTD Megatron rising 5-pack Generations Frenzy/Rumble I may be wrong on some of these, so bare with me.
