Namecoin is the only altcoin with a strong reason to exist. Most other alts are very slight variations on a theme, and I don't think that's a good reason to exist. *Because* LTC is the second most popular coin, and because of the short block time, and super low fees (in part because of the lower value of LTC) I think LTC has some value, but it's still just a slight variation on BTC.

If one of the proof-of-stake coins does things "right" (no central checkpointing, prevents gaming the blockchain, etc) that would be very worthy of people's use, but I am unaware of a proof-of-stake coin that avoids the above.

In short, I think Namecoin is clearly the best Altcoin, as it offers something new, maybe LTC as a third.

I predict LTC will continue to be #2 though, because people never listen to me ;-)