Start with a color. I have to admit that my favorite part is painting.

My son is 5 and his room is evolving from an ocean fish theme to a space theme. At the moment most of the fish are down and maps are up on the walls. I have some world maps which are lower and will eventually have celestial maps higher on the walls. I am looking for some retro space artwork.

The room is blue including the wood floor and the furnishings are basic and should take him through junior high. Keeping the metal elements black, the woods dark, and colors in the room blues, lime green, and orange, even with the theme change.

I agree that working a theme around a color would be a good option for you. If you prefer not to make everything so monochromatic, you could even choose a color theme (primary colors, tropical colors, "outdoorsy" colors, etc). You could also try a "shape" theme like stars, dots, stripes, etc.
Or you could center the room around their initials. You could find a large N and F and put them up above their beds. If you can't find large letters you could always try painting some or ordering monogram decals online.
Have fun!!

Start by finding two different comforters with similar colors (maybe orange and blue or blue and brown or light green, light blue, and navy). Then choose a shared muted color to start your decorating. I wouldn't worry about going theme-y as kids quickly outgrow. I would pick a kid-friendly basic color scheme that they can update and accessorize throughout the next few years.

Even adult colors look fine when you add shapes like circles. You can also pack a little punch with the lighting, curtains, rug, or other accessories.

Color YES, but let the kids help it is their room. I believe they have things in common. Video games, favorite characters from them or games. How about a bulletin board for all their special things, ribbons and awards near their bed.
Then the challenge, find magazines, expecially one like Lego' Bricks. I can almost assure you both like these colorful bricks. I am not sure if you can find those wonderful stick ups but if not maybe you can paint them. They are only blocks and the intructions have great pics with lighting.
I have always loved primary colors for kids. When my daughter 2 and son 7 shared a room tempoarily, they had Mickey Mouse and the gang. Brit had baby Mickey in her crib set, and Brian had a twin bed with the larger Mickey and friends. It lasted 5 years, then we put Brian into the boys room (then ages 7, 12 and 17) Yep 5 years apart.
I also like the idea of initials, you can get wooden ones on line that are 8 inches, or just paint them if you can above their beds.
You have a great opportunity here, talk to them, go window shopping and write down the OH WOWs and look at that game and get idea's from your kids. It's probably the only room they have a say in decorating. Don't forget the bean bags for a cuddle corner to read with good light above. Hanging or spotlight for in-house is a good choice.
Now, get going and let your mind run wild.
MKJ

I agree with everyone above, and I would emphasize color. My daughter and son share a room, and we chose light blue as an overall color to tie everything together. They both have light blue bedding, but with different accent colors. I tend to find inspiration in fabric.
For what it's worth, I don't think you have to design a themed room for the boys. Talking to them about what they would like might help you feel more excited, and finding basic ways to pull the room together--coordinating or matching basic needs in the room (furniture, bedding, wall color) will get you off to a great start. They will fill in the rest.
Good luck! Hope to see what you end up doing.

The most inspiring books I have found for children's rooms are the books by Judith Wilson, starting with Children's Spaces:

http://www.amazon.co.uk/Childrens-Spaces-Zero-Judith-Wilson/dp/1841721204/ref=sr_1_3?ie=UTF8&s=books&qid=1253193010&sr=8-3

This book of hers is also great:

http://www.amazon.co.uk/Childrens-Room-Essentials-Judith-Wilson/dp/1841726842/ref=sr_1_24?ie=UTF8&s=books&qid=1253193064&sr=1-24

When covering children's rooms, she always deals with shared rooms -- in a really fun way. In fact, the shared room she featured in the first book listed, a bedroom for the son and daughter of Suzanne Good of "The Rug Company" fame, is what inspired the design of the rooms for our children. Ms.Wilson is English, and so are many of the rooms she features, so take heart, as the UK has lots of wonderful sources (especially used and vintage).

Good luck!

Thanks so much everyone! Especially to MsChatelaine for the book recommendations, I picked up some nice bright paint samples last night and we're going to see how they work in their room :)

A little late to the table here, but I'm putting together a shared room for my boys, ages 9 and 2. Using the colors of a little button up shirt both boys wore and elements of Calvin and Hobbes to decorate. (Wagons, robots, spaceships...) It's been a lot more fun than I'd anticipated. And it screams boyhood without being theme-y.