For me, I'm going to say:
Half Life (and HL2): I just didn't see what the big deal was with these games. I played them, beat them, and thought they were slightly above average FPS games.
Portal 2: I really, really, really liked Portal, but I thought Portal 2 was horrible. The gameplay was good, but I thought the story was complete throwaway garbage, I hated the voice acting, and I felt like half the levels (or more) were just filler. I played it a second time on mute, and it was a little better, but still too much of it felt like filler.
Call of Duty (series): I enjoyed the first two, but after that I just didn't care for the series. MW did a decent job in trying to pull it into the modern setting, but the levels were too simple (though they looked good), and it hasn't pulled out of that rut since (especially the map layouts). I've seen modders put out better content that the CoD sequels.
Halo (series): I enjoyed the first game, but the sequels were all either rushed out the door, or quick cash-ins.
Final Fantasy 7 & 10: I thought 7 was horrible and 10 had great combat attached to an abysmal hold-you-hand-story. I'd add 9 in there, even though I liked some of the character/world design, but most people didn't like it, so I wouldn't call it overrated. (I've only played 1, 6, 7, 9, 10, so I can't say how the other games are)
Command & Conquer: Red Alert: I absolutely loved the original C&C, but RA was, IMO, one of the biggest let downs in my gaming career. The story was horrible and it lacked any of the charm that made the original game great. The cut scenes felt tacked on, and the game itself was awful. Though I will admit, I loved modding the mine vehicles into Flame Tanks...then I LOLed when the AI actually started building them (as they never would build the mine vehicles).
I'm sure there are others, but these are the ones that have always stood out for me.