Optimus Prime: Best: I say Laser Prime from G2. I love this figure... I desperately want Scourge. Ah well. Worst: Energon. Just... sacrifices too much for his combining gimmick.
Megatron: Best: Animated Leader, hands down. Worst: Would've been his original BW dino version, but then the movie came along. This dubious honor goes to his Voyager version.
Starscream: Best: Shame I can't put Classics or MP Screamer here, as I love them to pieces... but Animated Screamer is quite great, I hear. I only have Activators, but ah well. Worst: Cybertron Supreme? I don't have it, but it's a toy that doesn't seem any more complex than my $4 Legends of Cybertron toy. Don't get me wrong, it's a great LoC, but as a supreme... not so much.
Soundwave: Best: Probably still his G1, shockingly. It's the only one that has multiple tapes, though I really, really like his Animated version. The paint problems, however, keep him from being my favorite. Cybertron by default is the worst... and it's quite a crap figure.
Grimlock: Worst: Toss up between his Energon and his BW version... I have to go Energon, since it manages to take the original design and make it worse.

Post your opinions and feel free to add characters.

Best Prime- Cybertron Prime, with G2 Laser Prime in close second, Classics running third
Worst Prime- Armada Prime With Robot Masters Prime in close second

Best Megatron- Animated with, Energon in close second
Worst Megatron- MP Megatron, for $100+ you shouldn't be afraid to touch the figure, G2 Megatron and Armada Megatron are duking it out for second.

Best Primal- Optimal Optimus
Worst Primal- Either the 10th Ann Primal or the Deluxe BM Primal

Best BW Megatron- The origional T-Rex
Worst BW Megtaron- The BM Dragon

Best SoundWave- G1
Worste SoundWave- Animated

Best BumbleBee- Classics
Worst BumbleBee- Activator Animated

Best StarScream- Classics
Worst StarScream- Supreme StarScream, just not enough bang for the buck. Outside of that though, Animated, what a piece of sh!t!!!

Best Jazz- Animated, just got him and realy like him
Worst Jazz- Movie Jazz, feel free to pick any one

Best Ultra Magnus- RID
Worst Ultra Magnus- Sports Label

Best Combiner- Predaking
Worst Combiner- Any of the Energon ones

Best JetFire- G1
Worste JetFire- Energon(Armada sucked too)

Best GrimLock- G1
Worst GrimLock- Energon

Best Hot Shot- Either of the Cyberton ones
Worst Hot Shot- Armada

Best Galvatron- Energon
Worst Galvatron- Armada

Best Nemesis Prime- All Of Them
Worst Nemesis Prime- They're all good

Best RatTrap- TM RatTrap
Worste RatRtap- BM RatTrap

Best BlackArachnia- BM BlackArachnia
Worst BlackArachnia- The first one

Best SkyWarp- Classics
Worst SkyWarp- Cybertron

Best ThunderCracker- Armada ThunderCracker
Worst ThunderCracker- Movie ThunderCracker

Best Cheetor- TM Cheetor
Worst Cheetor- BM Cheetor, Supreme Cheetor

Best Rhinox- Tankor
Worst Rhinox- the initial one

I know there are alot more, but I can't think of any more bots with more than 2 versions off the top of my head.

Best Megatron :: Animated
Worst Megatron :: Machine Wars

Best BW Megatron:: TM2 Dragon Megatron
Worst BW Megatron :: Original T-Rex

Best Soundwave :: Music Label
Worst Soundwave :: Cybertron

Best Starscream :: Animated
Worst Starscream :: Movie

best optimus: classics
worst prime: energon

best megatron: masterpiece
worst megatron: titanium war within

best starscream: energon
worst starscream: movie

best ravage: alternator
worst ravage: energon

best grimlock:animated
worst grimlock: RID

best jazz: alternator meister
worst...: movie

best prowl: RID
worst prowl: energon

best smokescreen: alternator
worst smokescreen: armada

Optimus Prime
Best, Classics Voyager, though G2 Laser is a close second
Worst, Energon

Megatron
Best, tie between Henkei! Megatron and Armada Megatron
Worst, Ti GI Joe tank

Prowl
Best, Universe Classics
Worst, Energon

Starscream
Best, Classics
Worst, going to have to say Animated Voyager

Grimlock
Best, Classics
Worst, Energon, I really want to like him, but I can't bring myself to get past the

Soundwave
Best, Cybertron, Music Label's a close second though
Worst, Ti

Jazz
Best, Cybertron BotCon 08 exclusive
Worst, Movie

Skywarp
Best, Classics
Worst, Cybertron

Bumblebee
Best, Classics
Worst, Animated

Thundercracker
Best, Classics BotCon 07 exclusive
Worst, Cybertron

Best of the Best

Optimus Prime- MP followed closely by Cybertron

Megatron - Cyberton followed closely by Cyberton Heroes Megatron

Grimlock - Damn I hate them all (Has yet to buy animated)

Prowl - Until I find a Universe or Animated I have to go with G1

Red Alert - Cybertron Defense

Starscream - Energon deluxe

Bumblebee - Animated followed closely by concept movie Bumblebee

Ratchet - Movie line (don't own any others)

Unicron - Armada followed by Cybertron Heroes

Soundwave - Cybertron heroes

Worst of the Worst

Optimus Prime - Altanators hands down

Megatron - Armada

Grimlock - Though I've yet to like any of them Energon is by far the worst

Prowl - Energon

Red Alert - Deluxe Cybertron

Starscream - Cybertron Supreme - Can't afford one

Bumblebee G1

Ratchet - None thus far

Unicron - Cybertron deluxe

Soundwave - Titanium hands down

Wow. I can't believe you've all forgotten the FAIL that was the Titanium GIJoe/Cobra Megatron. Even the Titanium WWI Megs is a wonder compared to that steamer. You could throw a MW Megs at him and he'd collapse into evenly sized chunks of fail.

I've only mentioned figures that I have opened. GIJoe Megatron is in the package for that very reason, hence he's out of the running.

Best Prime- Cybertron Prime, Great articulation with even greater gimmicks
Worst Prime- Energon "Fattimus MegaZord" Prime, what a crap piece.

Best Megatron- Animated Leader Earth Mode... hands down
Worst Megatron- Titanium GiJoe Megatron.... wobbly pile of dung. Although Movie Leader Megatron is an extremely close second.

Best SoundWave- G1, untouchable... mostly because there's not many of him
Worste SoundWave- Animated, sadly a letdown

Best BumbleBee- Movie Concept Camaro....
Worst BumbleBee- Animated Deluxe, QC stunk and he looked fat.

Best StarScream- GF/Cybertron Voyager Screamer... delta seeker FTW
Worst StarScream- Armada, what a clumsy design

Best Jazz- G1, I'm old school.... shoot me
Worst Jazz- Movie, either one, doesn't matter... they're both crap

Best Ultra Magnus- Animated so far looks to be a blowout
Worst Ultra Magnus- Titanium G1, it reminds you that even G1 Magnus can look good

Best Combiner- LioKaiser (that's right, I pulled a Japan reference)
Worst Combiner- Tie between the 3 Energon turds

Best JetFire- G1, Macross crossover love
Worste JetFire- Titanium WW, what a messy alt mode

Best Grimlock- G1... nuff said
Worst Grimlock- Energon, but at least he was better than Swoop

Best Hot Shot- Cybertron by far
Worst Hot Shot- Armada by far

Best Galvatron- Energon, perfect G1 homeage. Universe may or may not bump this though
Worst Galvatron- Cybertron. Didn't care much for Megatron either

Best Prime- Classics - a new spin on the original
Worst Prime- Go-Bot Prime - looked more like Sideswipe than Prime

Best Megatron- Animated
Worst Megatron- All the movie ones tie for worst, with bendy-neck monstrosity TM2 Megs as runner up

Best Soundwave- G1
Worst Soundwave- Titanium

Best Bumblebee- Classics
Worst Bumblebee- Goldbug

Best Starscream- Voyager Cybertron
Worst Starscream- G1

Best Jazz- Animated
Worst Jazz- Movie

Best Ultra Magnus- Titanium, at least until the Animated toy comes out
Worst Ultra Magnus- Battle-in-a-box

Best Combiner- Railracer
Worst Combiner- Mega-Dinobot

Best Jetfire- Classics
Worst Jetfire- G1

Best Grimlock- Animated
Worst Grimlock- Energon

Best Hot Shot- Cybertron
Worst Hot Shot- Energon

Best Galvatron- Classic
Worst Galvatron- Any of the Megatron repaints

Best Cheetor- Night Strike or Universe
Worst Cheetor- Supreme Snarl-n-hiss Cheetor

NM

Couple more...

Best Hot Rod/Rodimus- Classics
Worst Hot Rod/Rodimus- G1 Rodimus Prime, Great alt, but just to much of a brick

Best Prowl- Classics
Worst Prowl- That Beast Wars thing(I'm trying not to mix BW with the rest of the line ups, but didn't they say they where one in the same in a comic?)

Best SmokeScreen- Alternators
Worst SmokeScreen- Armada

Best IronHide- BotCon TowLine redeco
Worst IronHide- Energon(nice figure, with the wrong name)

Best RamJet- Classics
Worst Ramjet- Armada

Best Thrust- WST(only mentioning bots I own)
Worst Thrust- Armada

Best LaserBeak- G1
Worst LaserBeak- Animated

Best Ravage- G1 tied with Beast Wars
Worst Ravage- Energon. I like that he looks like he looks like Voltrons kid, but that bot mode...

Best Scorponok- sorry G1, but I gotta go Energon
Worst Scorponok- Movie, I wanted to die when I saw that bot mode!!!

Best Waspinator- Fox Kids Transmetal
Worst Waspinator- Thrust

Best Devestator- G1
Worst Devestator- Energon/Classics

what's with all the Energon gestalt hate? sure they were 3 bots instead of 5 but they are posable as hell...

Assuming they can stay standing and hold together. There are some areas where they deserve credit, the connection ports are very solid, and working the larger robot body completely into the team leader is also nice.

They are poorly balanced, overly bulky, and the energon hands and feet tend to jump off at first chance. The RID and Beast Wars combiners where far better as the smaller robots actualy transformed into into eachother to creat the larger more solid robot. The Engeron Combiners where just a few smaller figures hanging off a larger body.

Plus they didn't look that good either.

I like the Energon combiner figures as separate figures, but as combined robots they just didn't make the mark.

Hot Rod/Rodimus Prime
Best, Classics (Hot Rod), Energon (Rodimus Prime)
Worst, Armada Powerlinx Hot Shot (yes, I'm counting the RiD, Armada and Cybertron Hot Rod homages)

Galvatron
Best, Energon
Worst, Cybertron

Jetfire
Best, Classics
Worst, Ti

Blackarachnia
Best, Animated
Worst, Beast Wars

Sunstreaker
Best, Universe Classics
Worst, RiD OTFCC 03 exclusive

Astrotrain
Best, Classics
Worst, BotCon exclusive

Ultra Magnus
Best, Classics, and the City Commander set will really add to it
Worst, Energon

Nemesis Prime
Best, RiD
Worst, Universe

My take

Prime
+ Cybertron Mode Animated (totally serious on that)
- Energon (speaks for itself)

Megatron
+ BW TM Megatron (if he counts) .. and it might be just because he was an awesome character more than anything.
- G2 Megs .. or even the Gigastorm gynormus paper weight in green with purple camo.

Starscream
+ Animated. Everything a Starscream should be.
- Armada .. Gimmick heavy, totally ruined the figure's chance at being something good. Electronic Backpack ftl

Soundwave
+ G1 .. like the TFA version, but Soundwave is meant to be something music oriented. (and oddly enough I don't need G1 Soundwave homages on my TFA to make a connection)
- Machine Wars .. nuff said.

Bumblebee
+ 2008 Camero .. All levels of total ass kickery
- TFA Bumblebee .. I can't pick on G1 for being a tiny little dorky thing, and classics was done up pretty well. TFA Bumblebee isn't bad, but he's far from great. Way too much kibble that gets in the way.

Ironhide
+ Movie .. total awesomeness.
- BW (the part that makes magnaboss) Terrible terrible robot mode.

Rampage
+ BW .. fitting and to the point.
- G1 .. cuz someone needs to bring up the rear.

Shockwave
+ G1 .. k well, he's simplistic and doesn't offer much of anything other than making noises.. I do like the alternator quite a bit. But a Mazada as a shockwave is pretty weird when you wrap your head around it. Really looking foward to seeing TFA Shocks do more than miss his targets though. I get such fan wood with that original voice attached. Still Megatron's batch.. and it's kinda lol.
- Energon .. again, enough said.

.. k thats all for now