I'm a big time downhill mountain-biker (40+ lb bikes going up to Whistler every weekend). I have a Yakima roof rack with the King Cobra attachments. Friends also have these for a WRX, B5 S4, Honda Odyssey, and our A4.
Pros: Fits any size of bike wheel / frame shape. Can take "heavy" bikes. Bikes seem most "secure". Doesn't interfere with lights, trunk, etc.. Rails can be used for other attachements or on their own. Looks cool on the car in my opinion. Bimmer still handles quite well at speed on the Whistler hwy, just a tad top heavy.
Cons: the paint on my roof is taking a beating, if you are shorter/weaker (ie. my wife, friend with WRX's girlfriend) it can be a PITA getting the bike up there, I'm the only one who hasn't "roofed" the bikes (fingers crossed).
I would consider a hitch rack of the type that are low mounted and you roll the bikes on (ie. holds the bikes by the wheels), my only concern is it kills your departure angle and those bikes seem to bounce awful close to the pavement when I see other cars with them. As with all rear racks, tail lights are somewhat obscured.
Never, never, never, ever use a trunk rack if you vaguely care about your car. Between the toasted paint, curled/bent trunk lids, and number of times I've seen a rack slack off and dump they are just not worth it.
Got mine at Rack Attack. Yakima and Thule stuff is significantly cheaper across the border - any future stuff I buy will be from REI.