Use some white lithium grease. Take a Q-Tip and put it in the hinges under the hood. Also put some in the hinges of your top, but make sure you don't have globs of grease around that can get on the top material. That should get rid of your squeaks for a good while (do it annually).
You could probably use WD-40, but it won't last long and is easy to spray all over the place on accident so I wouldn't recommend it.
As for rough roads making noise, it'll take a Cadillac or other such luxury suspension. The Boxster's suspension is very tight so you'll get road noise in rough situations.
