Comparing apples to apples, let's assume that you will be comparing the Bose 5.1 to a Cinema system with a decent budget subwoofer. The Bose satellites will not have enough extension to reach down to the highest frequencies of the sub, leaving a range of musical notes that will not be reproduced...at all. The Bose subwoofer module is not really a subwoofer at all and will not produce any really deep notes. Call it "sizzle and boom".
The Cinema don't really have all that great extension either but I find with my Cinemas that I get pretty good results crossing my subwoofer at 120Hz. Small, on-wall speakers generally have such limitations but as such, the Cinema is one of the better sounding solutions if you need wall mounted speakers. Depending on the price difference between the Bose and the Cinema, you can afford to buy a pretty killer little sub to go with the Cinema for the same or less money, maybe an SVS PB10. The Cinema/SVS combo will kick the living snot out of any Bose system, every time.
Plus, once you buy Bose, there is no upgrade path. You are stuck with whatever you have or replace the whole thing. If you go with the Cinema route, you can upgrade the speakers or sub at your pleasure whenever you can afford to. Bose = NO, not ever.
Definitely go with the Cinema series and the best subwoofer within your budget.