There is a bunch out there, but they aren't as well-known as some other web-comics are, yet. I can only give links to the lesser rated ones, but
google will give you the right adresses if you put in both title and authors, so here you go:
There is
Pandect, by Dina S., that is shounen-ai and stays PG-13, but is still clear about the character's involvement... *cough*
heart (It is a fantasy, romantic epic story)
You can also check out
Vampirates, by Jones. More of a 16+, it's clear enough not to let you wonder what those boys are doing in that bed. ^_~ (Vampire-pirates! How much sexier can you get?)
Those two are updated at least weekly and have been going on for a fair time already, given them a solid background already. For more recent (and slower to update) shounen-ai/yaoi web-comic, you can find:
Venom Fang by Dry Ice. It is still early on in the story, but it sure looks promising. =) (Magical, ancient asia)
Graceland by Okori, hosted on comicgenesis, is rated M for violence and explicit contents/hintings, and should appeal if you are looking for something darker. (Fantasy, action, dark)
Salad Days, by Chira and Muu. Even though we aren't there yet, I *know* it's meant to be shounen-ai and *will* be. Authors aren't denying anything either, so that's a good sign. The style isn't a very popular one even though I believe it's pure genius, if extremely confusing. Try it anyway, you'll like it!
There is also Psy-Matykz by RuuiCh4n (boys band, teenagers) , which you can find on y!gallery for explicit things, as well as the user thundertori (who recently published one of her brillant works, go check her out!)
Last, there is still "classics" of shounen-ai webmangas, like
Clipped Wings.
biggrin I hope you'll find something to your liking. They all are gorgeous to look at and have interesting plots. They'll fill your weeks right in.
3nodding 
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