Hey, I'm starting a new project of retiling my bathroom floor. When I pulled up the old tile, I was planning on using the old underlayerment, which was wood, over the subfloor. It was sturdy and sound, but I noticed water damage right next to the tub. I have to replace the underlayerment. I thought maybe this time I should use cement board, since it will stand against moisture and seems to be the recommended underlayerment. I just have one problem. The old wood that was under the toilet was 3/4 thick, to give it that added elevation. The rest of the floor was 3/8 thick. What do I do in terms of, if I do decide to do cement board: thickness for these areas. Or-should I just go with the wood again..? Seems pretty simple but I don't think so.

Was the subfloor under the toilet maybe replaced some time in the past to repair some other water damage? I can't think of any good reason to raise it an extra 3/8ths of an inch. It sounds like we're talking about vinyl flooring or something other than tile as well.

If you're laying down tile this time around, you'll want the floor at all one level. When figuring the thickness of the subfloor make sure to allow for the thickness of the tile and mastic so the height of the toilet mount works out. If the fitting works out to be too low, though, there are expansion versions of the old wax ring that work out well without having to re-plumb.

There are a couple of long threads on this board about different types of underlayment by people who know a lot more about it than me.

Good luck!

You need to patch the floor up to the orginal height then go over it with the cement board.
Be sure to put down thinset onto the plywood before your place the cement board down and screw it every six inches through the plywood to the studs. That will give you a nice solid floor. Its lots of work but even more if you have to go back and fix any cracks in the tile and grout later.

The first thing we'd need to know is what kind of finished floor you are installing.

I plan on doing stone tile and no, there wasn't any subfloor damage before. The underlayerment that was used on top of the subfloor was the particle board, from the feedback I've been getting, it seems odd they use wood as an underlayerment for tile, in a bathroom.
I am wondering now, if I can put 1/2 plywood on the subfloor (to make up for some of the thickness) around the toilet area and then put the 1/4 cement board down and tile on that. The tile would sit flush with the flange. Is that too much extra work?

No its no odd at all that they used the wrong stuff. It happens all the time.
If you decide to use any wood at all other then cement board, and in my opinion even with. I would cover the floor using Kirdi. Its a water proofing membrane that will stop any moisture from getting through the floor. It is simply put down on the floor with non-modified thinset cement. Then the tile, stone or what ever material you decide to put down gets set in another layer of thinset again.
You do not want the toilet flange to be flush with the floor. It must sit on top of the tile. There are flanges available to attach that can be adjusted to raise over the existing new floor height.