I don't own one, but this Amazon discussion suggests that carpet does affect the board's scale, but using the included risers will negate the effect of thick carpeting. Failing that, a hunk of plywood would probably work.
It sounds like you've already decided on the GTX 260. To be honest, at those price comparisons I'd probably choose the Nvidia, too, mainly for the much lower idle power consumption. And I didn't know that there was a version of the 260 that didn't exhaust out the back?
Intel, in a landslide. It's faster than the Phenom in every category (save for some instances of video encoding), is more energy efficient at stock speeds and overclocks better. The best aspect of AMD right now is its superior motherboards and chipsets, but that's more in the realm of HTPCs and budget dual-cores, not the power-hungry Phenom.
The 8600GTS used to be a low-midrange gaming card, but now is a bit outdated. It might have some value to someone trying to reduce power consumption (such as someone with a cheap/low-output power supply), but even then there are better options. For the same price or lower, you could get a 9600GT, HD3870, or 8800GT, which are superior to the 8600 in every way - in fact, the 9600GT and 3870 even use the same amount of power as the GTS. There's really no good reason for someone interested in gaming to go with an 8600GTS anymore.
Nearly full hard drives can slow some things down, such as Web browsing (no space for temp files) and defragmenting. I'm not too sure what other effects it would have, though. Having an extra internal drive won't slow down your computer; in some cases, it actually improves speeds (such as when used in RAID). Internal vs. external is up to preference, especially if the second drive is strictly for storage (i.e. not used for RAID). The Velociraptor beats out 3.5" drives like the Seagate in speed (fastest consumer HDD available) and power consumption (worse than laptop drives, better than desktop drives except the WD GreenPower series). It's too new to know much about its reliability.
You're the only one who can answer that question. This bit-tech article suggests that you'll see a 5-15 fps increase. It doesn't sound like a big increase to me, but it's your $200.
I am the owner of a Special Edition Falcon, and it really can be a fun, unique controller for games (esp. Half Life 2, though I want to get the gun attachment to make it even better). However, in its current state, it is not up to par with mice for general use. Since the arms move in and out as well as side to side, you can think you're moving the cursor while actually doing nothing. You have to have enough desk space to keep this in the proper position for mouse use - keeping it off to the side is a good way to develop RSI or a cramped neck. In addition, since there aren't any mouse drivers available for it yet, you have to keep the NVent software open and in the background for general mouse function.
I don't think this device has any shot at displacing a mouse. This is a specialty product, made for gamers looking for something new and geeky. It would also be a great device for 3D modelers, but I'm not aware of any drivers for that use.
It's certainly possible. You'd have to aim for low-power parts - MiniITX, external power supply, etc. Mini-box.com is a good place to start, though you'll probably balk once you see how expensive a MiniITX mobo can cost :)
For inspiration, look at the Ultimate Case Mod list.
I would actually recommend the 2600xt over the 8600GT, but only if the XT has GDDR3 memory. The differences between the cards aren't that great, but the 512MB 8600 cards come with GDDR2 memory, which is inferior to GDDR3. If the XT has GDDR3, it's a better buy, since that extra memory won't do much on cards like these.
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