1.) Myst
2.) Super Mario RPG
3.) Sam and Max Hit the Road

1) Fallout
2) Prince of Persia (Xbox versions 1 and 3)
3) Solitare

A Top 3 is nigh impossible but here are three games that come to mind:
Vagrant Story - Awesome setting, tone and art direction. Also some of my favorite music in any game.
Final Fantasy Tactics - Great battle system. Rich political story of betrayal. Addictive. And for those keeping score, this is the same team that made Vagrant Story and Final Fantasy XII.
Planescape: Torment - Quite possibly the best written game ever. The story is unparalleled.

1. Crusader: No Remorse
2. Deus Ex
3. Wing Commander III

Mine would be, in order of life wasted
1. Civilization
2. Star Control 2
3. Jones in the fast lane (PLEASE PLEASE PLEASE MAKE THIS ONE WORK AGAIN!!!)

I really think my No.1 lucky purchase was the £4.99/$7.99 purchase of SEAL Team from a Woolworth's store 'damaged' bin full of broken packages, etc, and in amongst it a (3 years old by now!) copy, undamaged, of the game! Have played it on and off for the last 10 years and there is still nothing like it ever produced!

Hell no, there hasn't been. I honestly thought someone would have attempted it by now. Viet Cong was a decent modern substitute, but nothing beats crawling through 2-3 kilometers of marsh on your 20th or 30th mission, KNOWING that if you get into a firefight, even with a veteran, hand-picked team, there was no way you were going to win... never enough ammo or time, too easy to get overwhelmed.
If you were ambushed, there was a very good chance that you would die in the kill zone. And there were no in-mission saves, even for operations that required hours of movement and watching... you'd just get taken to your funeral.
There was a real sense of desperation, followed by a sense of loss when you finished the campaign (which contained about 80 missions, but you only got to see 30-40 on an average playthrough IIRC).
In addition to my (well-loved) set of 3.5" disks -- I think there were 3? -- I buy copies of this game whenever I see them. I think I own three or four. The original with the huge camo box and manual is still my favorite though. :-)
Sorry for the hijack. Just love the game. :-)

Deus Ex, System Shock 2, and Total Annihilation (with Baldur's Gate 2 receiving an honorable mention, of course).

SEAL Team is worthy of hijacking any thread..... !!! Oh, and I have the big box camouflage version!

i couldn't pick three. so i'll pick groups of three by genre.
strategy:
romance of the three kingdoms (NES version) - probably for nostalgia reasons more than anything else.
civ iii, heavily modded
medieval 2, total war, heavily modded
adventure:
BAT II: the koshan conspiracy
i have no mouth and i must scream
blade runner (for the visuals alone)
MMOG:
ultima online
eve-online
federation 2
FPS:
stalker, heavily modded
oblivion, heavily modded
f.e.a.r.
RPG: (more than three)
darklands
fallout
arcanum (i overlook its many flaws because i love its setting SO much)
planescape - torment
star control ii
random:
hardwar
SI's football manager series
out of the park baseball series

In no order:
Deus Ex
Planescape: Torment
System Shock
I put together a web page listing all my favorites across a lot of years of gaming a couple years back should anyone be that bored (don't worry, no ads or junk):
http://gaming.bitspring.com/halloffame/

Without any order:
+Half-Life 2 - this game is simply brilliant ! I really enjoyed the story :]
+Fallout 2 - the 1st Fallout game I have ever played :] It's epic :]
+Tactical OPS: Assault on Terror - seriously this game is much better than any cs :]

i cant believe i forgot to mention grim fandango.
>_<

The orange box (ya I know its 5 games but oh well.)
Planescape
Monkey Island 4

Not bored at all, but still went to have a look and was impressed. You've been around a while! I would mention some titles like Under the Root, but I know gamers would say 'what?!'! :)