I go below 90 degree. I go until my legs touch my calfs, which happens to be where my hamstrings are stretched as far as my body will comfortably allow. I used to go to parallel, but I found that, as Rippetoe suggests, when you go really deep, you can utilize the bounce caused by stretching your hamstrings and glutes.
Its all about foot position in determining how deep you need to go before your reach the bounce. I have my heels about 1.5 inches in from my outer shoulder, and toes point about 30 degrees (looking down at my feet forms a 60-60-60 triangle). Just make sure your knees track your foot position during the whole squat, and the bounce will feel very natural. I recommend reading Starting Strength for good info on this topic, that is where I learned from. You might need to adjust your foot position a little as your anatomy differs, but I am more comfortable with feet a tad closer than what other people use.
Play around while the weight is light. If you do some high reps, such as 20 reps, then your body will tell you where to put your feet. Just make sure you follow three rules 1) always having your knees track your feet, 2) driving with your hips, and 3) keeping the back straight. Other than those, play around with the other variables until you find a spot where you can go deep and having it feel natural.
