I don't think we should be bothering counting virtual console versions here since they're automatically the best versions of the games being emulated (since they offer perfect emulation, with better image quality and temporary save states)
So aside from that, here's my contributions.
Killer 7 (GCN, PS2)
Definitive version - GCN
PS2 versions suffers from slowdown and aliasing and also has some censorship.
Banjo Kazooie (N64, 360)
Definitive version - None
The 360 version runs at a solid 30FPS as opposed to the N64 versions variable 20-30FPS and runs in HD, but there are a number of problems with the port. The intro is completely fucked up (out of sync movements, missing elements like Kazooie fighting Grunty etc) as is the fake ending (Banjo and Kazooie don't run back home), the camera controls are somewhat borked (the camera isn't as responsive and the 1st person mode awkwardly uses the 2nd stick), the changes to the note collection system make Click Clock Wood and Rusty Bucket Bay way too easy and ruin a lot of the fun of those levels, the enhanced draw distance makes finding items too easy now (since the lower draw distance was used to hide these items a lot, especially in Bubblegloop swamp) and a few of the enhanced HUD elements are a bit wonky looking. Plus the classic Nintendo logo intro is missing (unavoidable sadly but it does look wonky now)
It also suffers from a nasty glitch that can make getting all 900 notes impossible (Bottles Bonus Game note glitch)
Banjo Tooie (N64, 360)
Definitive version - None
Again the same thing applies here but the port is much better this time around. The framerate is again solid (and it's a bigger deal here because the N64 version's framerate was fucking terrible, 5-30FPS in no time flat!) and of course it runs in HD but again there are some problems. The intro is messed up again (though it's not as bad as in BK 360), the camera controls have been fixed though. Stop N' Swap is a complete waste though and adds nothing new to the game (woo a fucking Gamer Pic, thanks a fucking lot!).
The biggest problems with the port though are two fold. 1, the FPS section's controls are shit. 1 little mistake ruins everything, why does the cursor reset back to the centre of the screen when you let go of the stick?! WHY WHY WHY?! This makes the final boss fight almost impossible! I can't believe they made such a huge fuckup!
2, The cheats are now useless. Remember all the fun you had with SUPERBANJO? Well, guess what? Cheats now disable saving! WTF?! I can understand making them lock you out of the leaderboards but why disable saving all together?! This effectively ruins the cheats since they're now useless!
Perfect Dark (N64, 360)
Definitive version - None
Yes, it's online. Yes it runs at 60FPS. No it's not definitive.
While the 360 version adds some much needed framerate improvements (thank god!) it's still not perfect and can slowdown from time to time. Again the port comes with problems. The controls are somewhat iffy. There isn't one control scheme offered that feels quite right (and none that allow me to hold the A button to access the weapon select screen. WHY?!).
What pisses me off more is the little gameplay tweaks that change the game. Secondary function changing is now instant (not necessarily a bad thing but I don't like remakes that mess with the original core gameplay like this), smoke clouds are not nearly as strong and disappear much quicker (gone are those times where you can let off huge explosions and fight each other through the fog), the motion blur doesn't stay with you when you die (I know that this makes more sense and some hated it but I think that it's a shame that it's not even there as an option. It was a big part of the original game that helped define it's character and it's a shame to see it go completely, it was always really funny to watch someone miserably try to shake it off!), Laptop Gun was nerfed (fuck you 4J!) amongst certain glitches being removed like the poison knife dead body glitch.
Also I'm not a fan of the graphical overhaul. Some stuff looks good like Daniel Carrington's new model but Elvis and Johanna look crap! (Johanna looks like a reanimated corpse and Elvis doesn't look cute anymore

) Having the Goldeneye weapons in multiplayer though is pretty awesome.