Magic - The first and the best. Also, probably the only CCG where limited play really works.
L5R - Love the theme so much, but there's so many little moving pieces it's too easy for the gameplay to get out of whack.
WoW - Just a Magic ripoff with more flaws than fixes, but the one great thing it had is the multiplayer Raid deck, where one guy plays a boss character and the other players try to bring him down.
VS - On one hand it's nice that combat is so central, but on the other hand it's incredibly dry and mathy.
I still think the best CCG is what your friends are playing. You need to have a couple of friends building decks and playing as well as yourself or the experience quickly goes flat.
It is incredible that Magic: the Gathering, Netrunner and Jyhad were all designed by Richard Garfield. They are three of the most different CCGs out there and three of the best.
Whoa...oddly enough it never dawned on me that all three were in my top 10...and all three by the same man.
Sadly, the same man that designed Xena, X-Men TCG, and Rocketville.