I'm not talking about illegal downloads or scans. I'm talking about stuff that started online and is good, legal, and free.
MegaTokyo is one of the most popular web manga out there-I would start reading this again if I could remember where I left off...400's? Anyway I met the creators in person at a Q and A at Sakuracon. I think I asked about Japanese culture and..their favorite colors...I think.
Katie Bair is famous in the cosplay community for her fabulous wig skills, she is also a manga-ka, and doll maker. She hosts a online custom wig store as well as online manga such as the one I perticularly like, Aesir Corp. http://www.aesircorp.net/
While looking around her sites I found this really good link page which mentions some of the more popular (or not) online manga I haven't read such as penny arcade and other fun sites. http://www.katiebair.com/links.html
Penny arcade is really popular, but I haven't got to reading much of it.
My friend has a web comic thats...well...amazing! Its about Elves and adventure and awsomeness! The The Chronicles of Everglade! http://www.elvenparadise.com/