In no particular order:
?. System Shock
?. Fallout 2
?. Chrono Trigger

1. Monkey Island 2: LeChuck's Revenge
2. TIE Fighter
3. Balder's Gate 2: Shadows of Amn

Hmm... In no particular order:
Final Fantasy VI (but not the GBA version. One poorly thought out 'comic' line butchered my favourite scene. The small piece of censoring that came from the Japanese GBA version didn't help, either).
Chrono Trigger
Umm... dunno what my third game would be. Could be Fallout or it's sequel. Could be Breath of Fire: Dragon Quarter. Shin Megami Tensei: Devil Summoner - Raido Kaz... whateverhisnameis vs the Soulless Army. And Lucifer's Call/Nocturne... I guess pretty much any game I've finished, as opposed to stopping part-way, as is often the case with me. Well, not so much those Flash escape-the-room games.

1. Freespace 2
2. Tie Fighter
3. Starflight

Aahhh Microprose, how I miss thee so...

Hey, it's a Starflight fan, with a name derived from the game, no less! (While I never played or even knew of the game until sometime shortly after playing SC2:UQM since Starflight always gets mentioned on the official forums, it's better late than never.)
That reminds me-I need to finish up the first game already (Amiga version in particular; the Genesis/Mega Drive remake changed up the gameplay so much that it gives me whiplash), but never got around to it. I'd even Let's Play it, but I don't think I could make it exciting enough.

YAY! :) As much as I loved Star Control 2, it owed so much to Starflight 1 and 2 that those are all-time favorites. :) Welcome to the party. :)

I prefer some of Starflight's aspects, such as the whole training-a-crew-to-handle-various-tasks thing and the general feeling that you were going on more of a general expedition until you learn about the Crystal Planet making suns flare in a systematic fashion.
On the other hand, the Starflight races just don't seem to have quite as much personality as the Star Control ones to me, which probably sways me that way more aside from having played SC2 first. It could be because they don't have unique fonts for dialogue, their ships all look identical save for when you scan then, there's no voice acting (though the original IBM PC DOS version of SC2 didn't have voice acting either), or maybe that I just find the SC2 dialogue funnier or more touching.
Ultimately, though, there's no denying that the Starflight series paved the way for Star Control II. I've even noticed that Paul Reiche III was involved with both, and perhaps other developers were too.
(Now, if I can find complete Amiga copies of the first two Starflight titles...Genesis/Mega Drive versions are rather common on eBay, but home computer versions are harder to come by, especially complete...and when one does show up, it's usually the IBM PC original with the more dated graphics and interface.)

1. Master of Magic
2. Ancient Domains of Mystery (ADOM)
3. System Shock 2

1. Planescape: Torment
2. The Secret of Monkey Island
3. Spellbound Dizzy

Wow, choosing three games is more difficult than I thought it would be, but here goes nothing:
1. Ultima IV
2. Vagrant Story
3. Ikaruga

Curse Of Monkey Island
Final Fantasy VII
GTA 3

If you mean Westwood's version I agree wholeheartedly, Bladerunner is my favorite movie of all time and this game made me feel like a giddy fanboy all the way to the end. I wish I still had my copy (hint hint).
After reading more comments Chrono Trigger would be in my top 5 at the very least, haven't played it in so long.

Fallout 2
KOTOR 2 (with all this cut content, rushed ending, the game had tremendous impact on me. Like a great book. No other game managed to do that)
Half Life 1

1. Civilization
2. Ultima Online
3. Planescape: Torment