Evil Genius really annoying without unofficial patch
Commandos 2 feel like the better commandos 3 with Destination Paris

There's a content restoration patch for Planescape: Torment that also fixes some bugs like when you get Boney (or whatever the skull guy's called) back from being kidnapped but his inventory's been cleared out

GOG fairly recent update for Messiah to switch it to 3DFX + nGLiDE from D3D made it playable for me for the first time

I believe there's been stuff for the first STALKER game too - not too sure...

Non-GOG:
KOTOR 2 and Morrowwind spring to mind

Every single Bethesda game?

Morrowind? I thinks it's perfectly playable in vanilla. Might want to use the graphic extender to allow for widescreen resolutions, tough.

Oblivion is getting closer to "games totally improved". I could not bring myself to play through it in vanilla state, since the balancing (auto-leveling of enemies) was totally off. There are numerous mods out there that fix this, I used Oscuros Oblivion Overhaul.

Also: Skyrim. Many people could play through it without problems, but I ran into a few bugs in the main quest that would have been show stoppers where it not for some helpful mods (unofficial patches) from the community. Still had to use the console twice to "repair" NPCs that were stuck in their scripts.

For Grim Fandango there was a "late" (but official) patch that made the elevator scene solvable on faster machines.
Didn't run into problems with FO3. But yes, Bethesda is infamous for letting the community fix their games.

That's what i believe in. I like community patches that fixes games, but i really don't like these restoration patches. I think that when developers decide to cut content for the final release, they do so for a reason.

Sometimes it's "kill your darlings". But sometimes it's a matter of time and making the release date. In Planescape: Torment there was an area (late in the game) that was clearly not finished. Texts were missing (cursor indicates description but nothing happens) and you could get stuck going into one of the areas since they forgot the exit. I'm glad there are restoration patches for that.

Some Skyrim mods add back NPC banter (i.e. guard dialog) that was (probably) accidentally forgotten. I mean there even are voice recordings for that and the lines totally make sense within the game.

Do tell! I never played it with any fan patches.

Its' very minor. The original release had no pause and play function which given that you are usually controlling 4 or 5 people over a large area is ESSENTIAL! The patch put that in which takes it from frustrating and impossible to challenging a lot of fun.

Holy crap, no wonder the game took so long to finish haha. I might have to try that soon. I kind of think Bloodlines deserves a replay with the fancier version of the fan patch too.

There's also the new point and click mod :D

You are lucky. I got a heap of problems :(

Ahhhh, I was playing the GOG version at the end of last year, I missed that. I stand corrected.

The races are not very different from the previous installments of the game, but I would say that they are pretty different from each other - not sure which you're asking about. With 12 races (or was it 10? I forget) there's bound to be some overlap, but every race is unique.

I didn't play enough to really try every race, but there's likely balance problems as well. The real imbalance is certain race/hero combinations like Undead/Necromancer or Demon/Summoner where you can summon permanent free units that benefit from all the racial research & upgrades. That's something the fan patch tries to fix with the timers on summoned units, but I didn't like it.

What of the three X3? Reunion, Terran Conflict of Albion Prelude?

I'm not finished yet AP, but the other two have lots of bugs, specially TC.

That wasn't my experience. I never bothered with the patch for my first play through. The output looked pretty good to my eye and I had no issues with the gamepad input. Perhaps I would have become dissatisfied if I had known how much it was upscaling?