ok...I used to be manager of the audio dept at a very large retailer here in michigan and here is my advice:
1. go to a variety of stores and listen to everything you can, everyone has different tastes in sound and no one system is perfect for everyone
2. bose systems arent bad, from what you said you are looking at one of the lifestyle series, which the only one of those worth buying is the ls30 or 35...both very pricy but but have things that only bose can give you, the question is do you need those things. "proprietary" bose features are subtle but some people love them. the biggest one is the feature that will adapt the speakers for any enviroment...this one is actually cool...you can put freakin buckets over the speakers and they will adapt and still sound good. (i saw more than one bose rep do this)....the higher end systems are also upgradeabe, which means bose will send you a disc if they develop new software for your system, dont forget that this doesnt mean you can upgrade to say thx or 7.1 surround because the bose head unit doesnt have the speaker outputs or onboard amps for that....the "acoustimass module"(subwoofer) is also exclusive in the fact that it is non directional, meaning you can hid it behind you couch if you want to and it will still sound as good as if it were in the middle of your living room, bad thing is that is sounds like an 8 inch sub, probably because its actually a 5 1/4".....bose is always coming out with exclusive features...but the other companies always follow suit shortly after....prologic 2 is a good example of this, pl2 lets you put a mono input into the reciever and get 5.1 sound out of it, all the good recievers have this now.
3. I highly recomend going with a good...not top end reciever...this is the piece where the technology changes the most....spend some money on it but dont go overboard...next years will be 200 dollars less and have more features....put the money into the speakers...and the sub...those are the things that you can always incorporate into your new system
If i was to design my perfect system i would have a good onkyo reciever (like the tx-sr600 that i have now)...going to a good center channel, polk makes some very nice ones in many different sizes so you can pick one that is right for your room, dont forget the center is what most of the dialog from your movies is going to come from and also the most visible speaker since it will be on top of your tv....for the fronts it would either be mirage or polk( i really like polk) i would go with towers since they give you really good sound and chances are the fronts are going to end up on stands anyways, alot of the high end towers come with built in subs if you are a basshead....the rears i would go with some nice directional speakers that arent too big since ideally they will be hanging from your ceiling....maybe another speaker for the middle for your 6.1....the sub would have to be a velodyne 12"....you just cant get better...for your dvd/cd/mp3 needs look into doing that from your pc, i have a pc in my living room just for that, that way i can find any song or movie i want in a matter of seconds
I am done...sorry if it was too much info