Learned manual, first car manual, current car manual, but the minivan my wife drives is an automatic.
I prefer manual. All other things equal, I would take a manual. However, if the car otherwise suits my needs, auto isn't a deal breaker.
The one problem I have in the difference is the misconception of the parking brake that has arisen from the popularity of the automatic transmission. It is not an "emergency brake", your hydraulic breaks are far better than the simple mechanical lever. It is a parking brake, meant to be used whenever you park. Just putting an automatic in "park" is like leaving the car in gear (via a parking prowl). It stresses your prowl and transmission. Manufacturers recommend using the parking brake no matter what type of transmission you have. I have found that automatic drivers tend to get into the habit of putting the car in park and leaving it at that. Then again, some manual drivers tend to just leave it in gear...
Maybe it is less an "automatic vs manual" thing, and a people who don't know or care enough about their cars problem.
Also, I don't know if it is just me, but when I do drive the auto, I sometimes tap the brake with my left foot trying to hit the clutch...
<.<
Just me? Alright then.