If this were a most overrated thread, I think I might be the one person listing Sid Meier's games, including Civ, which I've bought every version of and played a decent amount.
But it's not, I'll scan the library for some ideas - though one off the top of my head is "Heaven and Earth", an outstanding puzzle game almost no one's heard of.
Casual games get short shrift, but I had fun with 'Peggle' and 'Luxor 2', so they might count as 'underrated' here.
The Last Express deserves credit for trying to do something new in adventures. Didn't sell well.
I haven't played them, but based on reviews and no attention here, might 'Incredible Machine' and 'Crazy Machine' series be underrated?
I think Uprising was underrated at the time, but it probably is all but unplayable now.
Uplink perhaps.
Jagged Alliance 2 was considered great by many who played it but I'm not sure it sold a lot.
Can't say first hand, but possible entries include "The Experiment", "Space Rangers".
I thought the Warlords series was great and underrated.