Hm...
Does Starcraft count as an old school game since it's still being played by hundreds of thousands? If it does, then well, that's my favorite game of all time so that.
I'm gonna avoid some obvious ones like Mario 64, Zelda: OoT/Majoras Mask etc, in favour of some (maybe?) slightly less known games:
1 - UFO: Enemy Unknown (aka X-Com). Fantastic game, I remember as a lil kid (like 6~ish) I had these PC magazines (we are talking 1995~96 here) and they had a review up for X-Com 2: Terror from the Deep and Master of Magic, and I wanted to play them sooooo bad... But I never actually played them until a few years ago. Absolutely brilliant game tho, and I had a hilariously memorable ending to it (assaulting the final enemy installation, I found my team down to one man so I decided to just use him to explore before I re-load... well, I walk into a room and notice 5 or 6 enemies, but I have no action points left so I end my turn.
Out of about a dozen shots, the alien soldiers manage to hit my lone hero no more than once - ship it! Surviving, somehow, through 3 rounds of this mess in what is one of the least statistically likely events ever - ok maybe not - my heroic X-Com trooper takes down the last 5 aliens in the base and ends the game for me

).
There's a free multiplayer version of the game you can download (fanmade) called UFO:2000 I think, it's quite fun (either by stacking up on ridiculous weapons and turning the entire battle field into a smoldering ruin or by actually playing seriously).
2 - Star Control 2 (aka Ur Quan Masters - you can dl it for free if you google it, ported for modern systems). Seriously, probably the funniest game I've ever played, I once saw someone compare it to Mass Effect (though this game was released in like 92 or 94, something like that), except that it doesn't have any of the useless sidequests or nothing (and don't get me wrong, Mass Effect is a great game). The Reapers and the Ur Quan are extremely, extremely similiar to be honest.
Anyway, some clips:
The Spathi:
http://www.youtube.com/watch?v=LEZ75L36m74
The Thraddash:
http://www.youtube.com/watch?v=9WsEh7oti3U