Primary reasons

If you're cracking, it's a fact of life that it's pretty difficult to find a suitable card (because cracking requires special driver modifications, and almost no manufacturer is willing to spend the effort to make the driver enhancements, because the vast majority of users never use it).

If you buy a good card that only works in a desktop, then sooner or later you'll want to use it on a laptop, and have to buy a second one. Or vice versa. A USB card guarantees you can use it on any computer.

Easier to get an external antenna connector

If you're cracking, you're going to want to hook up a larger antenna eventually. So RP-SMA (or similar) is a must.

However, if you're looking for a laptop card, it's almost impossible to get a PCMCIA card with an external RF connector. (though if you can find one with MMCX, you may do well) (U.fl connectors exist, but are rated for only a handful of matings)

BUT there are a number of aircrack-compatible USB wifi cards with RP-SMA!

Easiest to extend

Even if you have an indoor antenna, you WANT to be able to move it around ~20-30 feet, especially if you have a desktop, because your computer may be located in an area of low reception. The only way you'll know if there's a problem is if you can move the antenna around a lot. There are three ways of doing this, and USB is by far the cheapest and simplest:
• RF antenna cable — just add extra cable between the radio and the antenna, right? Nope, 2.4ghz gives LOTS of loss for every foot of extra cable, so you don't want to use more than 10' of cable, and even then, you'll have a much weaker signal than otherwise.

  Okay, so you've accepted that the radio and antenna need to be as close to each other as possible. But you can move the radio far away from the computer too, right?

• Cat5 — a POE-driven radio is the de-facto way of putting a wifi radio on your roof. Cat5 is cheap and can go 328ft before needing a repeater. BUT, this means that the radio has to have its own OS, and have web-based configuration and such. Which means that it's more complex and expensive than USB radios. (that said, the Bullet2 is sexy sexy sexy and astonishingly cheap)

• USB — USB can go 16.4ft before needing a repeater (AKA a cheap hub), and can go up to 80ft (25m) with enough hubs. You don't need any fancy web-based configuration, nor do you need to figure out how to get aircrack/kismet to work inside the radio itself (insane!). The card appears as if it were local, giving you a normal (non-constricting) environment to do your cracking in.

  USB is more of an indoor solution, but if you're willing to shell out for an an adequate rooftop system (remember there are several "hidden" costs like lightning arrestors, and all the mounting hardware), you can probably afford a decent indoor solution too. (and since they have functional differences, you'll probably want separate ones)

Smaller reasons

USB wifi cards, even ones without external antenanns, are more versatile than other cards — they can be integrated inside some very creative ad-hoc antennas. (here's a waveguide cantenna version)

If you become successful at cracking, realize that some of your friends and family will ask you to help you find their neighbor's passwords when you visit. (the only step you need specialized hardware for is the password-discovery phase... after that, you can punch in the password to any normal wifi card and connect)

If you have a PCI card, forget it. If you have a miniPCI/E card, you have to bring your laptop with you. If you have a PCMCIA/ExpressCard, then you probably still have to bring your laptop in case they only have a desktop or there are other issues.

But, if you have a USB wifi card, then all you need is the card and a BackTrack CD, and you can do your cracking on any computer.