If you are building a smaller home you are in luck, you can use audio gear that is hidden, distributed, and installed in the walls. you can either buy or build thin 4" deep subwooofers that can be built into your wall with only the speaker and port visible with a grill over it. you can also get some nice quality speakers installed for the rest of the music or even surround sound.
Also you can use a whole house music system to a better advantage than the 3000 sq foot home can. Newer high end systems come with 2 fm/am tuners and a XM or sirius tuner built in. Add a mp3 server and all your audio gear can fit in a shelf up in a closet.
already built home? then get under couch subwoofers (or better yet build them) or at the least get and install some "shakers" to add to your couch or chairs for that deep bass effect that does not bother the neighbors. The great part is, smaller spaced need far less sound to be full and enjoyable. buy quality over quantity. a set of small but good 6" shelf speakers in a small room will sound better than a set of huge coffee table sized monsters. Bose 601's and 301's are very good sounding speakers for a midrange quality speaker.... I personally go shopping for speakers at a musicians store and look for "studio monitors" they always sound better than anything at a best buy or stereo shop.