Good one! I adored #1 and #2 was so bad it was actually an embarrassment to crap! :D

Duke Nukem 2
Far Cry 2
GTA 2

Games which got enhanced over time and where I went back to a previous version:
Win War II (if I remember correct I didn't like the style of v4 and went back to v3)
Kaiser (didn't like the new style)

Final Fantasy 6 and 7, especially 7: FF6 started the decline of the series, and while still decent, it has many flaws (excessive cutscenes and poor game balance) and failed to live up to its predecessor. FF7 took FF6, removed the redeeming factors, made the problems worse (Whose idea was it to put Knights of the Round in the game? Who thought that was balanced?), and reduced the party size.

Also, in terms of the Dragon Quest series, 5 and 8 are overrated and among the weaker entries in the series (though still far better than the worst of the Final Fantasy series).