Water behind the headrests...
 

Whenever it rains, water collects somewhere behind the headrests (mostly behind the passenger seat). While driving, I can hear how it runs back & forth behind the driver's seat and the passenger seat -- sounding like it's an inch deep. Since this is something that happened quite recently, I suspect there might be some drainage that's clogged. Any help appreciated, (it's a Box '98).

-- peer

When you say "water collects somewhere behind the headrests" Is it the area under the clam shell?,if this is the case check the drainage holes here.Open your roof a little (a gap of about 10 inch or so between the windshield and roof front)under the half open clam shell you should then be able to gain access to two drain holes one either side of the engine cover area,blocked drain holes might be your problem.

Your problem does sound like blocked drain holes. You can blow out the clog with compressed air.
I had a similar problem, but never heard water. My problem turned out to be a tear in the plastic window. When I got the GAHH top with the glass window I never had water again.
Don't ignore this. If water gets under the drivers seat, you can destroy the computer (don't know the exact name for this).
A very costly problem.