Depends on the car. On a luxury sedan, like my XJ6, an automatic was all that's available, and it suits the car perfectly. On a car like the PT Curiser, the stock automatic is sloppy and slow. On cars like my PT Cruiser and my Fiat 124, the manual lets you get the most out of the engine. On a big engine musclecar, it's really not an issue, as either way, you get a lot of performance, with the automatic giving you more consistency.
In a performance car where consistency and the last little bit of speed is important, a modded automatic is going to be faster. But not every car has the parts available to get the most from the trans. Domestic cars have this market sewn up, ith shift kits and custom valve bodies, and performance torque converters available (the same way the imports have fuel maps, engine control modules, etc available). So for a v6 or V8 domestic, an automatic with $45-50 worth of parts will shift faster, firmer and more consistently than any manual, and give you as much fun driving, and you'll actually be more in control (though you won't have to move your left foot, except to use the brake).
On smal engine cars with narrow powerbands, I prefer manuals, and stay away from automatics unless I don't care about performance. On mid level engines, I like manuals but have no problems with good automatics. On bigger engine performance cars, I prefer autoamtics but don't mind manuals. On race cars, I prefer whichever is best suited to the particular job.