In case anybody else happens to be curious, I just took a look at BMW's own stated performance figures for its 3-Series cars.
The 320i comes with either a 5-speed manual, or a 5-speed automatic. 0-100 km/h times for each are as follows: 8.7 sec. for the manual, 9.8 for the auto.
For the 325i (6-speed auto, 6-speed manual), the times are 7.1 for the manual, 7.8 for the auto.
For the 330i (6-speed auto, 6-speed manual), the times are 6.5 for the manual, 6.7 for the auto.
In each case, the automatic has a shorter final drive ratio than the manual (which should make it quicker), but the gearbox ratios are actually a little taller for the automatic. So it seems that overall gearing is probably pretty similar (although I didn't bother to do the math to figure it out exactly).
I'm not sure how to explain the results, really. It does seem clear that the differences between the two become less and less as engine torque increases, but I'm not really sure why this would be the case.
Maybe it all simply boils down to the extra weight of the automatic. As each car gets a bigger, more powerful engine, it also gets heavier, and the weight penalty for the automatic becomes smaller and smaller. For example, the automatic 320i is 2.5% heavier than its manual sibling, the auto 325i is 2.0% heavier than the manual 325i, while the 330i automatic is only 1.0% heavier than the manual.
Anyway, slower acceleration is but one (and by far the least important, IMO) disadvantage of an auto tranny. As Davidm and others have mentioned, there's plenty of more important reasons to prefer a manual to an automatic.