Totally joined this site just to post this (though I am going to thoroughly take a look at everything else).
By far the best Yuri webcomic I ever came across is The Lounge. Summary from the site: The Lounge follows the misadventures of the sexy Lounge Manager Italy Ishida. Italy inherited The Lounge, an anime/games/comics/coffee shop, from her ailing father. She is assisted by Max, her rice obsessed protege, and eventually more characters who join the staff
The primary yuri is between Italy and one of her High School friends (they are now adults). School friend appears about a month into the comic and they start to hook up about five months later (Poor Max).
Started off back in 2002, it ran regularly till 2009 when the authors father passed away. After a year away, he began writing again until he started missing updates in 2012. From there its been sporadic, and he hasn't for over a year. Until NOW!!! (Thank you all soooooo much for inspiring me to go check it again) Seriously I squee'd hard when I went to type this post and saw that he had posted a page for Monday. I grew up with this comic and it is seriously beautiful.
On a side note, The primary reason the Lounge hasnt updated in the last year is the author has begun a new comic, The Hunters of Salamantra. The comic is not yuri (yet) but it might become yuri (I am hoping) based on the authors preferences and some of the characters actions (see linked page).
Also the author writes some smutty comics for slipshine (several of which are yuri) if you are interested.