What a cool space! I love built-in shelves/spaces like that. One of these days...

Well, shelves are the obvious choice, for your books and other decorative items as well as a place to put things like cable boxes/gaming systems/routers. You could do some as cube shelves, you know, like these:

Eco-friendly 4 Cubby Bookcase in White · More Info

(I don't mean that you would actually stick a shelving unit in there, I mean you could do that style of shelves.)

You don't say how deep the cavities are, which does affect/limit the amount and type of stuff you could put there.

Family photos would be nice, too; maybe get one blown up to fill about half the space, and then a shelf beneath it with a few more pictures?

Something like this could go in one or more of the spaces:

3 Tier Diamond Matte Black Metal Display Shelf · More Info

Really, it's about what items you want near you, and want to look at every day, as well as about the style and look of the rest of the room. It's difficult to say, "Put these modern-looking shelves and decor," in there if you are going for a country/traditional type of look, you know?

You could also consider putting doors over some of the shelves, which would break up the spaces a bit and add some interest/decor all on their own. Glass doors with interesting frames, wood doors with cool pulls or detail work, that sort of thing.

Here's a nice room where they've put in similar shelves to the ones above, and they have the colored background, too:

White Entertainment Center With Blue Accent · More Info

If you collect anything, that might be a good place to display it?

What style are you going for, what things do you like?

I hope that's at least some help! I'm sure if you tell us what types of things you like and what the look of the rest of the room is--what kind of look you're going for--then others will have more suggestions for you.