i'm currently running a full klipsch set myself.
i'm running a pioneer vsx-30 receiver which has been a blast to deal with. you don't need anything this expensive but i wanted the OSD instead of just faceplate controls.
for speakers i'm running the klipsch quintet IV (5.0) set. they are satelite style speakers but are very well built. great if you want to set them on a desk or shelf. personally i have the L,R and C on my desk with the two rears on my bookshelf behind with cable ran under the floor.
for a sub i'm running the klipsch 450w sub SW-450. its a ported downward firing design. build quality is typical of pretty much all subwoofers out there. its not as fancy as the speakers but its by no means subpar at all.
as for how i feel about my system? its an absolute beast. definitely a huge step up from standard computer speakers. as for other speakers klipsch makes... i've heard some of the bookshelf models and floorstanders but i do not have the space for them and the price was higher than what i wanted to pay. the nice thing about the set i picked is its all matched in a box but its in a whole different league from HTIB sets.
as far as the hdt500 set is built... i believe i saw that one in a store and passed on it because it didnt impress me as much as their normal products. after having the klipsch set now i would look favorably towards it but as i've never owned or heard that set i would still be just a little wary.
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now as for the big question....is this all overkill?
for JUST bf3? yeah it a pretty big way. personally for most people i just suggest getting a $50-200 logitech set as that is more than good enough for the typical enthusiast.
in order to recommend a more expensive system normally people will be using it for other games, movies, music, etcetera. however, if sound is really that important to you its definitely not a bad call. after all you can keep the system around for many years to come and hook it up to an entertainment center in the future.
i'm a little bit the same i suppose... in total my pc may have cost me $2500. i already had my 40" lcdtv and 20.1" monitor from a different build so the costs for them aren't much of a factor. however, i did go out and spend at least $1300 on sound equipment not because its necessary but because i wanted to (and i dont regret it at all).
so i say...if you want to splurge...then do so
if you want to go budget....then do so
it all comes down to what you want from your system, how much you want to spend, and if its all worthwhile to you.
in regards to the yamaha receiver you mentioned...i've heard yamaha is good choice but i have no idea about particular models. one thing you will want to do is make sure what the maximum w output is per channel and compare it to the speakers you want to buy.
in regards to dolby... this refers to dolby surround which is just surround sound decoding.