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 ;-)
Read my post on Namecoin being the Platinum of cryptos.
http://www.legitcoinage.com/?p=90Interesting article, I'm glad at the end you mentioned that scarcity isn't the only thing to look at, since that's what I was thinking to myself through the first part of the article

. I think Namecoin deserves an analysis of its value based on its value as a distributed DNS, its value as a general K/V store (some people are talking about building in a torrent tracker, and other features, since Namecoin isn't technically limited to DNS), along with scarcity, and its development problems (NMC has a leadership issue right now).