I've done the spline joint that widget recommended but now I use biscuit joints because they are easier to do. The spline required careful alignment of the pieces for the spline cut and if it's off a little bit the piece is ruined. With biscuit joints if you make a mistake just move down a little and do it again.
I did the rabbit joints for a while and they are great but a lot of dust from the router or else several passes with the table saw. Again, the biscuit joints seem to be the easiest and fastest method.
I use 1 1/4 brad nails from a porter cable BN150. Much better than screws and they are a bitch to pull out.