Well, of what's out right now Zits is probably my current favorite. I would say Foxtrot, because it's my all-time general fave (tied with Calvin and Hobbes), but ultimately his weeklies have been mostly retreads of the same jokes he's been making for years. I'm glad he's still writing, though, as he'll occasionally come up with a cool original/hilarious joke and that's certainly better than nothing.
PBS isn't my FAVORITE, but I like it a lot. It's actually even funnier with Pastis' commentary, so the treasuries are where it's at.
Another HUGE favorite is Cul de Sac- although one couldn't mistake them for each other, it definitely reminded me of Calvin and Hobbes when I was first reading it, and in fact, Bill Waterson thought it was the best thing since sliced bread. Sadly, it's been discontinued because Richard Thompson has Parkinson's Disease
So technically it's not modern, but close.
Another favorite is Baby Blues, although they've kind of just been using the same jokes over and over, too. I mean, the author's kids have to be adults by now. I can imagine there are only so many stories to use, so I can understand it.
Brevity is awesome (if a little inscrutable at times), Speed Bump is usually pretty good, F-Minus is always worth a look, Rose is Rose has gotten a little TOO damn cutesy, but still cheers me up form time to time (some of the older stuff is creative genius, if you ask me), Stone Soup is always a delight (it's like For Better or for Worse meets Roseanne, or maybe it's just Roseanne), I used to love Rudy Park (is it still running?), The Buckets can be pretty good, and I like Pickles as well (although I can't find any collections out there for some reason).
A lot of people like Get Fuzzy a lot but I remain to understand its appeal. I understand that a strip doesn't have to have a real pun at the end, and can be funny throughout, but they've just never done much for me. I like Garfield more than I'd care to admit, especially the years 1998-1998, but like so many others, I believe Davis (or Davis' team of writers) has finally run out of ideas, too.
Yes, I am a funnies nerd. Shaddup.