Ok here goes-I would def. go with waterproof outdoor speakers, and just bolt them to the rollbar like I did, works great, they are nice and clear, and are pretty much submersible, also do not require building/buying a box, and are very easy to mount.
Car speakers, as stated earlier, when not the paper cone type, are pretty much waterproof from the front, the rear however needs to be protected. If you figure out some way to get speakers in the dash, tell us, I've been trying to figure something out for speakers up front for awhile.
In terms of a sub and amp, go with something not too expensive, especially the amp. It is nice knowing that if something gets wet or muddy, you aren't going to wet your pants worrying its busted. I am planning on mounting my amp inside the sub box and completely sealing and waterproofing the box. As you can see in the pics, its pretty nasty, the box is crap itself, a friend made it for a different friend as a truck box, it just happened to work pretty well in my cruiser.
I got the headunit at Circuit City for $200, $50 less than list cause it was an in store model and one year out of date. I would have gotten a cheaper one, but I wanted one that had a subwoofer preamp, this is very nice so you can really adjust the sound output of all the speakers at the head, just leave the amp gain on all the way and use the subwoofer preamp control on the head.
I really like where this box goes, and its reversible, I have the sub facing back in the wintertime when the hardtop is on, it makes the sound richer bouncing off the rear of the top, and its better for throwing some tunes out the back in the parking lot

. In the topless months, I turn it around and it provides a nice thumb right in the back of the seats.
Cost list-
$200 head unit
$50 for MTX Thunderform 4000 12" MSRP ~150-200 (from friend)
$0 for box/200w 2 channel Optima amp (from friend) MSRP~150 I think
$0 for Boston Acoustics Weatherproof patio speakers MSRP $350 a pair (traded baseball equip to friend, I blew out my rotator cuff)
Total $250 plus a baseball bag, bat, and glove.
You could probably do a 2 waterproof rear speaker w 200w amp and 12" sub with decent cd head for about $600, it really doesn't take much to fill up a 40 with sound, especially one with a hard top. Included are some pics of the temp. stereo setup.
Oh yeah, a friend has a headunit in a tuffy, I personally really prefer it in the dash, mine's gotten soaked 3 or 4 times, it normally just quits working for a few days and then when it dries out it starts working again. :dunno:
To get it in the dash all you need is a pair of pliers and a die grinder. It fits perfectly between the dash pads, the face revolves out with 1/4" clearance on each side.