Hmm. Feels unfair - I could easily do a top five from both "Beast Machines" and "Robots in Disguise" without much difficulty. However, here we go:-
1) RiD Optimus Prime/CR Fire Convoy: Love the look of the design in all three modes and he's got some good solid articulation for his era. Add in gimmicks that actually feel like they make some kind of sense with his vehicle mode and we are onto a winner.
2) Universe Skywarp: One version of this mold was going to make it in, and Skywarp is elected by virtue of having the best colour scheme. This is the mold that got me back into buying Transformer toys (when it was released as Jetstorm). A cleverly engineered transformation, and a sculpt that is good enough to sell that this thing might actually fly. He also looks great in humanoid mode as well.
3) Beast Machines Stryka: Having tried an attempt at a six-wheeled armour vehicle vehicon with Blastcharge, Hasbro provided us with an apology in the form of Stryka, and a very good apology it is too. A fantastic sculpt, full of character, and a fun little gimmick.
4) RiD Scourge: Taking one of my favourite "Generation 2" toys, painting it black and giving the trailer a nice shiny silver chroming... On to a winner here - looks very nice in the dark colours, and is fantastically poseable. If I was still a kid he would have been a certainty to get the slot of "evil leader" toy in the collection.
5) Beast Machines/Robots in Disguise Obsidian: Cheating I know, but I love the mold and I think both the green-and-green and "cow copter" colour schemes are quite effective on him. Blessed with a lovely range of poseability for his era, and with a simple but fun transformation, Obsidian is a real winner for me.
Bubbling under: Universe Whirl - a good fun mold from the original line, in a much better colour scheme than his original release. Spychanger Scourge - an mini-replica of Scourge where they have done a superb job in maintaining the sculpt, great stuff. Night Slash Cheetor - lean, mean and with an eyecatching colour scheme, best Cheetor toy by a mile. Honorable mention - RiD Skybte, because I like his character more for my attachment to his character than to his toy.
RiD/Car Robots Brave Maximus - I'm crazy about citybots and this is also the best repaint of any Transformer, ever!
RiD Optimus Prime/Car Robots Fire Convoy - For the same reasons as mentioned by Nick.
RiD Scourge/Car Robots Dark Prime - Ditto
Beast Machines Primal Prime - Okay, I know the character is utter fanwank, but the toy looks sweet. Not only that, but they took a design flaw from the Optimal Optimus version and replaced it with a better mechanism.
RiD Rail Racer/Car Robots JRX - I really like all three train modes and the combined robot is very well designed and thought out.
Honourable mention goes to RiD Air Attack Optimus Primal - I don't have one yet, but eventually I'll track one down. I know he's officially RiD, but he'll be going in my Beast Machines display as the definitive version of the character.
"Understanding is a three edged sword: your side, their side and the truth"
Kosh Naranek - Babylon 5
I don't have many figs from this area, yet. I have both versions of R.i.D. Prowl, it's a decent mold, but I preffer the chunkier style. I preffer bits of the car to form legs etc, instead of the legs unfolding from inside and there being loadsa kibble on his back and so on. I did have R.i.D. Megatron, the multi-changing one with the hand mode. It was a decent fig also, but traded it a while ago.
I was the one who let you know, I was your sorry ever after, '84, '85. Give me new toys and I'll decide, but I'm really only after, '84, '85.