I like both for kind of different reasons, with an edge going to manga probably.
Manga in general is fun to read because you get huge chunks of story at a time, and it's typically at a really good, professional level because it's done by, well, professionals. You don't see either of these things as much in webcomics where the majority of them are done by hobbyists and thus vary wildly in quality, as well as usually update slowly.
On the flip side, webcomics are a lot of fun to read for other reasons- I love reading color comics and with webcomics it feels like it's easier to interact with the creator and even other readers by way of comments and the like.
For ones I like a lot...
Manga- MAR, Dragon Drive, +Anima, Soul Eater (currently rereading as I got a few new volumes for Christmas ), Magi, Zatch Bell, etc.
Webcomics- The Witch's Throne, Hexameron, Weak Hero, Pomp's Pomps, Unfamiliar, etc. etc.