Inverted in Amazoness!, which is set in the mythical Amazon city of Themiskyra in which men are not allowed to step foot. The only men who have shown up so far are nameless mooks who exist only to be killed by the Amazons in battle. There is the matter of Eutropia who is biologically male but psychologically female.
In Ctrl+Alt+Del, of the 4 people (and one penguin) living in the main characters' house, Lilah is the only female.
Inverted heavily in Drowtales, where the female characters heavily outweigh the male ones both in numbers and importance. This is a deliberate attempt to correct the male-heavy presentation of the Drow in the Forgotten Realms setting, despite their matriarchal society. It also easily demonstrates just how flexible female characterization can be at its best, and how unnecessary this trope tends to be.
The first two arcs of El Goonish Shive are basically just Elliot and Tedd doing stuff with Sarah appearing once or twice. However, this ends up massively subverted in the end as the next three major arcs introduce five more characters, only one of which is male.
Hanna Is Not a Boy's Name has an almost all-male cast, with only one of the main characters a girl and another woman being a recurring villain.
Homestuck does an excellent job of averting this. The core groups of characters, such as the kids and the trolls are perfectly gender balanced. This tends to hold true for minor character groups (such as the Exiles, and, to a lesser extent, the guardians) as well. The only places where it's in effect are the Midnight Crew (0:4) and the Felt (1:14). Additionally, ascensions to God Tiers have been keeping the balance too, even with a degree of leaning to females.
This is lampshaded early on in the Insecticomics where Kickback claims that viewers had complained that the comic didn't have any female characters and uses this as a justification to vote to change Laserbeak's gender to female. Somehow.
The Order of the Stick's eponymous group consists of four males (all of whom are better in melee than ranged), one female (ranged), and an elf (whose androgyny is a Running Gag, and who is not very good at physical combat at all), though other female characters have since become prominent supporting cast members, notably Celia.
Inverted in Questionable Content, where Marten was for a long time the only male character in the main cast, with five female characters all making frequent appearances. The cartoonist tends to lampshade this in The Rant whenever a new female character shows up: "Because all I need is another female character".
Six Pack of Otters is something of an interesting case. We have not yet been introduced to all six of the Otters that the title implies...but of the five that we have met, four are male. And the fifth, female Otter's presence is felt mostly by the other four (male) cast-member's reaction to her: she's not unseen, but she hasn't had a whole ton of screen-time either. Made unusual because the author of the comic is female, and the setting is a college campus (i.e. there's no particular reason that the setting should include few females).
Linda Concarne is the only female regular in Triangle and Robert. Of course, no one can accuse her of being Ms. Fanservice, since the characters are all shapes. She's a rectangle.
Erin is pretty much the only female character in the Magic: The Gathering webcomic UG Madness. Then again, it IS a webcomic about a game with a predominantly male player base. Erin herself is very much aware of this, and thus has a very strong drive to prove herself.
Terra the earthworm in 1/0. This is lampshaded by the fact that the Interactive Author initially didn't want any female characters because he wanted his male characters to remain romantically frustrated. When it became clear Ho Yay would be the inevitable result, he relented and added her â€” and made her a lesbian, so the guys would still be frustrated.
The entire cast of 8-Bit Theater contains a grand total of four female characters (White Mage, Kary, Bahamut's witch girlfriend, and princess Sara), only one of which is a major one. She is also the White Magician Girl, not quite a main character and by a wide margin the least powerful character. However, this is almost undoubtedly a result of the source material or a deliberate parody thereof.
However, in the end she kills the Big Bad without the help of the men, who were too incompetent to do it themselves. This does not change the fact that every other important character is male, save one villain.