Some of it was to preserve historic rivalries (Dallas should stay in the NFC East, for example, and I say that as a Dallas fan who doesn't really enjoy playing six games against a Division that annually has two playoff teams when it doesn't have three). Some of it is just insane, the most glaring example being the AFC North/South/East:

North:
Pittsburgh
Cleveland
Cincinatti
Baltimore

East:
New England
New York
Miami
Buffalo

South:
Indianapolis
Tennessee
Houston
Jacksonville

See anything wrong? Like the fact Indys historic rivalries with the rest of the East were shot to hell by placing a team on the Great Lakes in the "South"? Wouldn't putting Miami in the South and Indy in the East make a helluva lot more sense? Or put them in the North and Baltimore in the East; that would make even more sense because it retains Miamis old Division rivals. Instead, Indy and the erstwhile Oilers were removed from the Divisions with their historic rivals and put into one with two teams that didn't exist twenty years ago, which, IMHO, has a whole lot to do with why Indy is the winningest regular season team of the decade (again, much like it was easy for SF to make the playoffs every year when they had one less divisional opponent and the ones they DID have all sucked; playing four games against the '80s Cards and Saints teams would give anyone a leg up on the playoffs).

Unfortunately, we just DID a realignment; Seattle isn't even in the same Conference anymore (and, boy, does Denver miss playing them twice a year right now... ) so don't hold your breath. Until we have eight 5 team Divisions another realignment is unlikely.