Below are the bedding choices I worked with in my twins bedroom theme, and shown are aqua and lime walls just to give you an idea of how each color might look. You wouldn't have to use such strong colors, lighter shades would work just as well. On the left is Scooby Doo Thumbprints set and on the right is the Barbie Princess Toddler Set.
General Decor
Use a low table or chest between them that they can share as a nightstand, or if you want them farther apart, get them each their own low nightstand.
If you can find matching beds great, but if not just use what you have or are able to get and paint them to match. That's usually enough to make them blend together in the room.
Either get a second hand dresser or a new unfinished one, and paint it white and paint the drawer fronts and shelves? You could alternately paint one aqua, one lime, one pink etc. and add some cute knobs or handles.
Or if you didn't want to do all the colors, just paint it solid white and use some of the stick ups mentioned below or some Wallies on there. Put Scooby on his drawer and Barbie on hers. That way they know which one is theirs.
I chose the Barbie Princess bedding for her half of the twins bedroom theme because it has the aqua and lime that the Scooby Doo Thumbprints bedding has, yet has lots of pink for your girly girl! Toddler bedding choices are few and far in between, and as of the time of this writing, you can get both of these sets at eBay very reasonably priced! And you really couldn't make them for much less, not to mention the time it would take.
Make some sort of division of his and hers in the closet, not just in the dresser. A couple of those hanging canvas organizers would work well in the closet. The Dreamtime Princess Barbie Poster on would look cute on her wall. It's a ballerina, and isn't quite as high fashion looking as most of the other Barbie prints. And that should be more than enough theme stuff.