Hi Nicole,
Here are some ideas (just my taste, so you may not like them!).
For the family room, I was going to suggest either a burgundy, cinnamon, or deep gold color as one option (although it sounds like you don't want to go in the burgundy direction) if you want to keep it somewhat tonal, but not all brown. Another idea, would be to use a green - perhaps a moss shade - not too dark, but not too light...would work well with the green, but add some contrast.
For the master bedroom, I have found that I personally like things to be less contrasting - more tone on tone, which seems somehow more relaxing. Perhaps a lighter or darker shade of taupe for the walls, and perhaps something in the same family, either darker or lighter for the master bath. I have seen a really striking bathroom in mostly white, with gray and silver in a recent Pottery Barn catalog, that made me think that might look nice too.
For the spare room, I'd probably go with either a buttery yellow or a warm beige (or mintish green if you really want color). You could then use with either a boy or girl and dress up with accent colors, etc.
good luck and have fun!