Ultima is a great answer. Mega Man was never that big in sales but well known enough. It's dead. Marvel Vs Capcom is another. Capcom vs series in general. Deus Ex and Red Faction. At one point in time Far East of Eden series was almost as popular in Japan as Dragon Quest. It was huge. The last game in the series was a remake of II on the Xbox 360. Japan only.

Socom.

Miss me some Suikoden and Castlevania

Uncharted

But i dont think it will stay dead. Maybe the grand return to the franchise will happen with ps6

I second this and would like to add the other 2 of the big 3 of western RPG, as in Might & Magic as well as Wizardry 

Thinking of the older ones, King's Quest(/Space Quest/Police Quest - which held on longer as SWAT).

Personally I miss Populous. And Lemmings.

Yeah, unfortunately, all party based CRPG IPs from that "Golden Age" era went into decline, and, bar games form 1st CRPG Renaissance spearheaded by Interplay in late 90s/early 00s, gave way to single character 3D action/RPGs.

Deadspace now since EA refused to do a new one or remake the 2nd.

As a guitar player, I never thought Guitar Hero was great. It always felt like a stupid kids toy to me, like one of those Hot Lixx guitars from the 80's, and I hated the trend with an unhealthy passion. lol

To the OP, my vote would be Syphon Filter. The first two games were great, imo.

Is it too soon to say Half-Life?
Ok, what about Portal?
Star Fox?
Metal Gear if we don't count remakes and remasters.
And Castlevania.