Since I'm a hybrid gamer (meaning I've played about the same amount of PC and console games, I found it too hard to decide on the best gameplay for all platforms. So I separated it.
For PCs:
The Ultimate DOOM: While the original DOOM from 1993 is great (after the patches of course, DOOM v1.1 refuses to run on a newer PC, even in DOS), the 1995 patch of DOOM makes the game even better. The level design is the greatest of what I've experienced in DOOM (I haven't had the balls/skill to get past DOOM 2 in Ultra-Violence, I ran out of ammo :doh
and Ultra Violence E4M6 easily provides the best pre Half-Life level design (wanna try it? Bump my links thread, which is in my sig BTW, and I'll post the game for you).
For Consoles:
Sonic The Hedgehog 3 & Knuckles: Yes Yoshi's Island is good and all (great actually), but I've logged morte hours into this game than any other pre-PS1 game. Considering I've played Chrono Trigger three times and the fact that S3&K can be theoretically beaten in 2-4 hours, this is significant. I've not only beaten the game with all four character types and emeralds (Sonic, Sonic & Tails, Tails, and Knuckles with 14 Emeralds each), but got a perfect score on each special stage and got over 99 lives, which causes a neat graphical corrpution where the lives counter is. This game is Sonic at his best.
Jam it back in, in the dark.
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Kaiten