Bad Company 2 doesn't limit itself to any particular thread count and I wouldn't expect BF3 to be any different. During a level load on BC2 on an i7 you will see 8 cores somewhat busy with threads from the application. I havent looked at it myself but that particular scenario makes sense because loading files into memory can be threaded per file/per part very easily.
I will soon get to witness first hand BC2's thread usage but most reviews say it will utilize as many cores as you can give it, but were also limited on core/thread capability at 8 to 12 atm.
Certain times the game might only have its threads going to 3 or 4 cores and at other times windows will have so many active threads going it wont know what to do with them. But other apps we run while gaming still as you mention have the chance to benefit.
I do have a cpu meter on my G13/G19 and watch it while playing games and when I had my AMD 4x4 running just basic stuff in the background while playing a game that could sometimes effect my performance. This was because they would either update or something else thus causing problems in games so I had to close almost everything, now this isn't to say a 4 core (talk about Hyper-Threading from Intel in a sec) isn't enough to run a game but the more background programs you can off load to other cores the less the less of chance these programs will effect your performance in a game, the more cores a game supports the less you have to deal with this problem as well.
BFBC2 does limit itself to Quad core so only 4 instructions per the recommended specs so having a 6 core will give you no benefit. I know you said it will support as many cores as you can throw at it but I'm sorry I could not find any official evidence to prove that, what I could find was this from
Techspot Performance In-depth article which said
The game appears to be using all four cores when available. Here we used a standard Core i7 920 processor running at 2.66GHz. Please note HyperThreading was disabled and a single Radeon HD 5850 graphics card was used. As you can see none of the cores are working very hard.
Here is the same Core i7 920 processor with two cores disabled as well as HyperThreading. As you can see neither core is maxed out, but the CPU utilization is much higher. So again, a decent dual core processor such as a Core 2 Duo E8xxx or Phenom II X2 should be enough to get the most out of your graphics card in this game. While it is quad-core optimized, the game is not demanding enough on the CPU to warrant it based on what I have seen so far.
This doesn't cover 6 core unfortunately but it does show that having a 4 core cpu greatly reduces the cpu load, here is what I found with 6 core cpu performance from
Benchmark Reviews with the Phenom-II X6-1090T it does compare against the i7-980X
Here we can see what I was talking about that the game will not be more efficient with more then 4 cores even with Hyper-Threading enabled. The BIGGEST problem with games is that a vast majority only support 2 cores and 4 cores is the limit for games (at this time). A little bit of word play is at work here, when they say Multi-Core support that is limited to 2 cores more often then not, which gets people assuming that it will support their quad core when it doesn't. The games that do not limit themselves to only 2 cores are ones that say Quad core specifically but that's the limit 4 nothing more. I just don't think jumping on the 6 core bandwagon is going give any one a dramatic performance increase in games and the info here supports that. Now granted this is only one game but for the sake of argument it's the one we have been discussing and I am limiting myself to this game. The only benefit you might see is if you like running stuff in the background, which normally gamers do not because of the unforeseen impact they can have on performance.
Just to prove that my i7 950 does not use the Hyper-Threading in BFBC2, I jumped into the game and was on the Heavy Metal map and got into a little bit of action but nothing major, here is what my Task Manager showed.
As you can see core 0, 2, 4 and 6 are the physical CPU cores and 1, 3, 5 and 7 are for Hyper-Threading. The thing about Hyper-Threading is that allows multiple instructions to be sent to the CPUs cores, it doesn't give you additional processing power like you would have with more cores. This isn't to say that it doesn't make your CPU more efficient however what it does mean that just having it enabled isn't going to change your game's performance unless it can recognize that additional instruction set, which again a majority don't. This is because they rehash game engines like the Unreal ED and until they update the engine or others like it to use Hyper-Threading or Quad/Hexa-Core CPUs this will remain the norm.
When I moved to the i7 I noticed I could run a few things in the background that I could not before and I am assuming it is because of Hyper-Threading, this is a distinct advantage Intel has over AMD because those background programs were no longer taking away direct CPU cycles away from the games themselves. The journey with Hyper-Threading has been a bumpy ride but they have worked most of the bugs out and it's worth having in my opinion, especially if your a hardcore or enthusiast gamer.
I do HOPE that BF3 can and will use more then just 4 cores and take advantage of that additional performance but I am doubtful, this is because the main stream is just now getting Quad as the standard CPU. I hope this clears up my position and gives any one else reading this a little more insight into this clouded situation.
EDIT: I forgot to mention that I still recommend getting the additional GPU and going XFire. The reason is that the CPU does calculate the physics but when your pushing the GFX especially with DX11/DX10 and you have a physics event like a building crumbling all those dust, smoke and particles need to be animated as efficiently as possible. The CPU is important and it most defiantly will cause you performance problems if it's not up to snuff I whole heartedly agree with you on that, but keep in mind that GPUs are now doing a lot more when it comes to DX11/DX10 instructions, so with out powerful GFX configuration to back up the CPU your going to cause a bottle neck and lose performance.