Correct me if I am wrong but it seems as if water can enter the space between the fender and the panel the speaker mounts to. The existing kick panels have moisture stains, and the drain tubes run through this area.

So, do ya'll use any sort of baffles to protect your speakers, and how do these affect the sound?

Right on.

 

I never did on any of my cars. And if you got water leaking there, you got more serious problems than a speaker

 

Yes water can enter there, not easy, but it can.
I got some pic I'll try find a post when I get home.
on a donor car I was taking pics with the fender/door off, to get an idea of how much work it would be to build an enclosure there extending into the empty fender area, simliar to a what a BMW did many years ago stuffin what I belive were 12's into the kick panels.
I'm not going for 12's just wanted a solid enclosed area for a little more low end coming from the front.

 

Yeah I mean I have two sets of the stock kick panels from two cars and all four of them have mild water stains on them. Something is getting in there. If the sunroof drains through there, then you got water in there.

 

Here you can see the sunroof drain coming out, if that for some reason was pulled back in a bit, ouch.

 

Here you can see the speaker magnet thru the hole I was thinkin of, but its for the door wiring to go thru, but again, if that rubber boot was ripped, it could let water in.

 

here is a shot from the inside, hmm... lotsa room to play with if the dash wasn't there, hehe