Going back to the Box's mods, to me it seems to make the most sense to go for a computer retuning, as people seem to get the most benefit and enjoyment for the money spent, from what I've seen on here, better power delivery, a few horses to gain, and also improving the fuel economy (though you're more likely to be putting your foot down more often afterward, so you'll only benefit from that last one when you're driving nicely). Exhausts, depending on what you buy, can do anything from just sound nice to netting you a few horses (with the aforementioned tune

), but they'll also likely save you some weight and turn the rear trunk into less of a furnace (if you didn't know already, don't put anything in the rear trunk that doesn't like heat, it gets toasty in there).
On the intake side of things there's a lot of controversy over the effectiveness of an intake mod. Some say stick with the stock box and only remove the snorkel, others swear by their new intake box. That one's entirely up to you. Now beyond the airbox, the plumbing from there onward to the engine is fair game and worth the time without breaking the bank. It may not gain you gobs of power, but the delivery of the power you do have will be better.