For Science Fiction I'd have to say Asimov's and Analog. I haven't read either of them in awhile (I drifted over to the dark side, ie Fantasy) but they always had quality science fiction. For fantasy there's the Magazine of Fantasy and Science Fiction. One of the nice things about those three magazines is they're more or less the size and shape of paperbacks, so they're easy to carry around.
But as far as I'm concerned, the all time best magazine for fantasy is Realms of Fantasy. It's big, it's glossy, and it's the only one I ever read cover to cover. I read everything from the letters to the editor to the game reviews. There's a movies column, a books column, and even a folktales column. The stories are always top quality. My dream is to have something published by them.