Just for the record: I'm mainly responding because y'all are monsters(!) and left out the most important one. The rest of my list is just set-dressing in comparison. ;)
Day of the Tentacle (AKA Maniac Mansion II: Day of the Tentacle)
was unquestionably better than
Maniac Mansion!
Indiana Jones and the Fate of Atlantis
was a lot more fun that
Indiana Jones and the Last Crusade
for me.
Vampire: The Masquerade – Bloodlines
turned out a better (or at the very least more memorable and beloved) game than
Vampire: The Masquerade – Redemption
And that despite Bloodlines releasing in "a ****ing state"...
I'd replay Secret of Mana (Seiken Densetsu 2)
over
Final Fantasy Adventure AKA Mystic Quest (Seiken Densetsu)
on any given day.
Final Fantasy Adventure was very nice, but didn't hold a candle to Secret of Mana.
I think most would agree that
Legacy of Kain: Soul Reaver
found more fans than
Blood Omen: Legacy of Kain,
be we're starting to get into territory where opinions would be divided.
Laura Bow: The Dagger of Amon Ra
was better than is prequel
Laura Bow: The Colonel's Bequest,
but a big part of that might have been more capable PCs and such...
Neither of them was great (or even recommendable) in my opinion, but your mileage might differ.
Populous II: Trials of the Olympian Gods
>
Populous.
It seems likely that some would also have opinions about the following games (but I'm not familiar enough with them myself, but I'm listing them for those who might get nostalgic for being reminded of them):
Star Control Vs. Star Control II
System Shock Vs. System Shock 2
Arena Vs. Daggerfall
Lufia & the Fortress of Doom Vs. Lufia II: Rise of the Sinistrals
Clock Tower Vs. Clock Tower 2
(These might be more known to people who know how to make use of an emulator... ;) )
But yeah: Games were fun...