Girl Genius has certain advantages to my personal tastes over Schlock Mercenary. It's a gaslamp fantasy, with romance and gorgeous Victorian-esque clothing and dashing adventurers and sexy men and women and airships and mad science and steampunk and humor and lovely artwork by Phil Foglio, whose art I've always enjoyed and -- well, in short, it's got a whole bunch of things I really like in a story. I expect I would love it even if it did not have many of these things: I love Buck Godot and I loved Foglio's Stanley and His Monster and Angel and the Ape and, well, I've liked pretty much everything Phil Foglio's ever done. Including Xxxenophile. But Girl Genius is especially dear to me.
Schlock Mercenary has far fewer natural advantages in winning my enthusiasm. It's a science fiction comic with some hard-sf elements, about mercenaries and wars and betrayals and explosions, and none of these are things I particularly love in a story. (I do like sf, but I generally like fantasy better, especially eclectic not-Tolkien-esque fantasy). Howard Tayler has worked very hard on his art in the many years since he started Schlock, with the result that I'd now describe it as "nice". As opposed to "abysmal", which is where he started. >:) In all seriousness, Tayler has a solid cartoony style now that serves the story well and is attractive. But it doesn't have the rich details that Foglio piles into his work and that make Girl Genius so delightful and rewarding to look at.
Schlock does have a couple of advantages over Girl Genius. First, my Schlock fix is there every day, not just three times a week.
Second, howardtayler and sandratayler both keep blogs. So do the Foglios, for that matter, but I don't chat with them via LJ and I do talk to the Taylers occasionally (they even read my LJ! Squee!) so I tend to think of them a bit more like friends rather than just "people whose work I follow". On the other hand, the reason I met them on LJ is that Schlock was already my favorite comic, so I don't think this predisposed me unfairly to like it. :)
Anyway, they're both great comics, consistently funny and entertaining, with well-thought-out stories and great character development. I recommend both highly.
But what I really want to know is: what is your favorite webcomic? And no listing all 30 or 40 that you follow, either. I mean, you can list them all if you want, but if you pick just one or two then I'm more likely to take a look. :) I don't read that many comics right now -- I thinned my list considerably the last time I changed computers -- and I'd like to add some new ones to it now. Feel free to repeat a recommendation someone else made already -- the more people like a given comic, the more likely I am to investigate it, too. You needn't feel obliged to give all the reasons you love it, unless you want to; a link suffices for a plug. :)