Thought this thread was going to be a little more specific than just another auto vs manual thing. Nevermind.
Entirely depends on the car really. If I'm to get beyond simply auto/manual there are several variations of each I quite like.
I like a nice mechanical-feeling manual change, like something is actually happening down there. One reason I'm so defensive of modern autos (aside from the fact they're simply very good) is that most modern manuals have a bit of a sloppy change that lacks tactility. Exceptions to this rule: MX-5, GT 86, pretty much anything made by Honda, Mazda. I also prefer a spherical gearknob - I find the trend for weirdly-shaped gearknobs pretty annoying.
Older manual transmissions can be fun too. By which I mean going back to the 60s and 70s in classic cars. Nice long, thin lever, typically a long throw, that mechanical feeling again, and usually quite a delicate gearknob that suits the long chrome stick it's usually perched on.
The best layout for autos I've used is Mercedes' current column-shift one. Just a small lever on the right-hand side of the wheel; click it down for drive, up for reverse, and press the button on the end for park. Frees up space on the centre console, and Mercedes always combines it with gearshift paddles too for manual control.
Jaguar's little knurled metal wheel is also really nice to use. Rises out of the console when you start, just click it round to the drive mode you need, or one extra click clockwise for sport mode. Again, standard paddleshift.