My favorite trail in South Mountain starts at the trail head just south of 24th st and Baseline.  It's the start of the Mormon Loop and when you connect up to the Mormon Trail/National Trail it extends the hike to about 4 or so miles.  Or at least that's what I have been telling myself.  First part is stair master-esque, then descends very gradually (perfect place to add a run into your hike), then ascends again (catch your breathe) and then gets a bit boulder-y and you can either straight up hike this or run.  If you want, you can take the offshoot to Hidden Valley and Fat Man's Pass.  I wasn't too impressed with either, but it is definitely worth a view and will spit you back out onto the National Trail.