I've had Manitou, Fox, Rock Shox and Marzocchi forks on my bikes.
Of them, Marzocchi is the more rigid with is pretty good at tracking, and has the better suspension feel, very plush on rocks and not much bob. Overall, the best fork I've used.
Rock Shox has increased it's quality and features since it was bought by SRAM. I have a Revelation and have nothing but good things to say about it. It has motion control, which helps with pedal bob and is very adjustable.
Fox, well, it's a pretty well thougth out fork. Plush and the dials are the best I've seen to date. While I had a 06 model, the 07 Talas offer 3 different travel distances (100-120-140) and it seems to be very easy to select the right one. On the other hand, on the 'zocchi fork, you seem to turn and turn to dial the right travel.
Manitou, I had a Black Elite and it worked fine, I had some oil leaks at the beggining, but I changed bike shop and the last one left it working pretty good. But I don't think it's at the level of the other 3.
But, it mainly comes out on your budget, your bike and what you want the fork for.
Some people prefer coil over air, and some air over coil. Air forks are generarily lighter than coil, and can be adjusted better for rider weight. If you're a heavier rider, you just put some more air pressure, and if you're a lighter rider, you let out some air. On coil forks, you have to change the coil to get the proper sag for your weight. On the other hand, coil is plusher than air, generarily. So for some harder terrain and drops, coil is probably better than air, although some new air forks are improving a lot.