Nothing has been as easily moddable as Half-Life, with the same install-base.
I suspect there's another problem with mods today: asset production. In Half-Life's day even I could hack out a semi-passable player model in a day or two. Nowadays, producing assets for games has been made dramatically more complex. In short, you really can't find a lot of people willing to produce that quality and complexity of art for free. The size of teams required to put anything together, as a result of this, has also put a lot of things beyond a mod team's modest reaches.
I think that's why a lot of the indie excitement is around casual and "low-fi" games like Minecraft. Assets have always been a major blocker, and when you embrace the fact that you're not AAA, you have a better experience with it.
Some games, yes. Epic foster an incredible community with their incredibly generous terms for licensing the UDK out to all. Skyrim will no doubt see a profusion of mods; the Total War games all have a healthy modding community; all Valve games are as moddable as HL2 was, given they... uhh... are still on the same engine.
There seem to be a lot of new Skyrim mods coming out every other day. Mostly cosmetic stuff, but I wouldn't be surprised to see more 'total conversion' style work soon.
I haven't really checked moddb.com since Unreal Tournament 2004 was the big online game, but it seems to be going strong.
Different genre and a few years old now, but Civilization 4 is supremely moddable with a very active community. Firaxis released the entire source code to the game rules engine!
I suspect there's another problem with mods today: asset production. In Half-Life's day even I could hack out a semi-passable player model in a day or two. Nowadays, producing assets for games has been made dramatically more complex. In short, you really can't find a lot of people willing to produce that quality and complexity of art for free. The size of teams required to put anything together, as a result of this, has also put a lot of things beyond a mod team's modest reaches.
I think that's why a lot of the indie excitement is around casual and "low-fi" games like Minecraft. Assets have always been a major blocker, and when you embrace the fact that you're not AAA, you have a better experience with it.