Know how to look through a blend file to figure out what's going on?
Then I've got just the thing for you!
http://dominodesigns.info/downloads/second_life/male_av_blend.zip
This is intended as a piece to learn from. I've not spent the time to perfect it, but it shows off all the key techniques you'll need for baking avatar textures in Blender.
The mesh is a single unified one with multiple textures. It's setup to bake directly to 3 different images, you'll need to add a fourth if you want to work on the head.
The main images are UpperBody and LowerBody, these are where the Blender materials on the clothing part of the mesh are baked to. There's also a "Dummy" image which is where parts we aren't interested in end up. Currently the head, left arm and left foot go here. These left parts normally map over the right ones so they are separated to prevent interference when baking.
There are a number of vertice groups setup for easy selection of the different parts.
There are a couple of displacement modifiers for wrinkles (using the avatar wrinkle bump maps from the source release of SL). You could edit those images or add extra ones for doing things like seams and pockets.
There's a rough dome lighting setup on layer two, so you can disable this layer when working and just enable it for the bake. It's not fine tuned, that's something I left for you to experiment with. I'd probably scrap it and do a proper one for a final piece

There are currently 3 materials, a default one on the head, and an upper and lower body one. You can add more and assign them to individual faces as your project requires or just alter / replace the existing ones. Which I'm sure you'll want to do as these are very quickly done just to show the techniques

The upper body one has a logo which is controlled by the empty "LogoPos" you can move, rotate or scale this to alter the logo. Tip: you might want to try Clip Cube option on the decal image
I think that's the key points covered, feel free to ask if you need any clarification on something.
Oh, when doing things like t-shirts, you'll need to apply the alpha channel to the final image in your paint package. The upper body sample shows how to do it in Blender, but you still end up with the base material showing, so that will need a touch of post production
