Since my CJ is nearly a daily driver, and I park on campus without doors most of the time, I went cheap and practical.
For the dash, I bought a pair of 5.25" marine speakers made by Boss. They have grills you can remove, and like any dash speaker they go in easier when you have the dash off. You can do it with the dash on, but it's not very fun (at least the driver's side speaker).
For the rears, the PO had a set of 6x9s in cheap boxes set behind the seats. They're easy to direct the sound, look like hell and no punk in his right mind would want them. Why change a good thing? I bought a pair of 6x9" Boss marine speakers and threw 'em back there.
The sound is great from all sides, even while driving without a top or doors at 60mph (fast as she'll go). I spilled an entire cup of soda on one of the rears and it didn't even flinch. I'm sure they could handle the rain, but I try not to drive on those rare days we get rain here. I'm more worried about the cowl seal and the rain ruining my hard-to-find-these-days cassette deck.
All said and done, it was less than $100 for the four speakers.