Funny, I am planning to do a video series comparing versions of games. I did one but its slipshod.
Basically, get the one that works for you. For example, I am happy with my gamecube version of RE4
I mean obviously in all but the extreme cases, versions are somewhat comparable. PS2 version of RE4 has extra content (the Separate Ways side-campaign as well as other things). Wii version includes these additions AFAIK as well as the controls that seem to be a huge hit with that version.
That said, it wasn't available until much later than the GC/PS2 versions.
What might be best is if you post what games you still need to buy, and we can help you determine the "definitive" version for you.
Here's a few games I'm having trouble deciding which version to get:
Pikmin - GC original or New Play Control. Unfortunately Pikmin 2 was never released as NPC in the states
Conker's Bad Fur Day - leaning towards N64 original as more "definitive". Has anyone played the remake on the xbox? it's significantly cheaper
Worms Armageddon - loved this game back in the day on the PC, wanted to get a multiplayer console version. Options: N64 (most expensive but what I'm leaning towards), Playstation, or the newer Worms 2: Armageddon for the PS3 or 360. I hate digital games but if they are a really great improvement I'd consider it.
Rayman 3 - Hoodlum Havoc - PS2 or GC...is there a significant difference? Yes I know they just did an HD remake on the PSN
Metal Gear Solid HD Collection - PS3 or 360...differences?
Also, I'm planning to get many of the HD collections for the PS3. I'm attracted to the upscaled graphics and single-package deal but I don't want to sacrifice gameplay (bugs, glitches, freezing, framerate issues, missing content). Of the following, please let me know if you consider the originals superior. For example, I've heard the Prince of Persia trilogy has freezing issues and such. And apparently the first couple games in the Splinter Cell trilogy are lacking inversion option (WTF?).
God of War Collection (PS3)
The Sly Collection (PS3)
Jak and Daxter Collection (PS3)
The Ratchet and Clank Collection (PS3)
The Ico & Shadow of the Colossus Collection (PS3)
Tomb Raider Trilogy (PS3)