The stock front speakers are 6 3/4" and my Polk EX365's were 6 1/2".  I literally cut the rim off the stock factory speaker to obtain a mounting point for the Polk's.

Polk EX365 mounted on the stock Toyota bracket.

Polk EX365 mounted in the front door.

Custom rear 5 1/4" speaker bracket cut out of 3/4" Baltic birch plywood.  Candido tipped me off to this trick.

Polk EX352 mounted in the rear door.  Stock rear speaker are 4".

This is a real simple set up and suits me fine.  It's not really even worth a write up, but I did want to show how the factory used non-standard sizes.  So any speaker upgrade will require quite a bit of custom work.

Update: 12-27-2002

I had heard that Boston Acoustic includes adapter plates with their 6.5" speakers to drop right into the odd sized Toyota 6 3/4" openings.  So I ordered a complete set of Boston Acoustics mounting plates.  None of these were a direct bolt on but could be modified to work just like I did with the stock speaker ring.  So I stuck with my modified stock speaker rings.  I milled them down further by removing the outer lip and smoothing out the inside ring further.  I then sealed the Polk speaker to the stock bracket/mounting ring with silicone for a tighter sound.  I'll probably pull the rears and seal them up as well.

Template for making the rear door speaker mounts.