New Midrange Gaming/Computing Machine- Need Advising

I am currently looking to upgrade, completely, from a machine designed some 4 years ago. It was a wonderful beast, but is falling behind now on what I want to use it for. I have a basic set of parts I need advice on, as well as whether it is worth it to buy now, or wait for some newer nextgen options are cheaper (DDR3, GPUs, etc.)

CASE: http://www.newegg.com/product/product.asp?item=N82E1681...
Heard good things mostly about thermaltake, although also heard it is overpriced rubbish a few times.

PSU: I already own an Antec Truepower 550W unit. Recent buy, works fine for my machine, would rather not spend money on a new one if not necessary.

MOBO: http://www.newegg.com/product/product.asp?item=N82E1681...
High rated on newegg, and I like having 6 SATA outs, and the numerous PCI ports. I want this machine to last 4 years, so I want it upgradeable. I do not know much about MOBOs though.

GPU: http://www.newegg.com/product/product.asp?item=N82E1681...
Heard good things about this one (EVGA 8800GTS). Do NOT have money for anything more, this one is already pushing my budget. Need advice on whether this is a good buy, or whether to buy cheap and wait for the 9xxx line to drop prices on the GTX.

CPU: http://www.newegg.com/product/product.asp?item=N82E1681...
The Intel Core 2 Q6600. It is between this and the duo. I game fairly heavily, but one of my hobbies is playing in Lightwave (same as Maya, or 3D-Studio Max, etc.) as well as photoshop and with other video making programs. The quad looked good, but I have heard something about stepping problems. Don't know what that means, need advice.

CPU HEATSINK http://www.newegg.com/product/product.asp?item=N82E1683...
A scythe infinity cooler. I will be attaching a second fan, one to push air through, the other to pull it out. Read this was a good deal esp. for overclocking quad core processors, something I plan on doing.

Memory http://www.newegg.com/product/product.asp?item=N82E1682...
Buying two sets for 4 GB of Patriot DDR2 800 RAM. It looks like these are good, middle of the road, and also overclock nicely. A must I hear for the Quad processor. Don't know though.

HDD http://www.newegg.com/product/product.asp?item=N82E1682...
I already own one 250 GB SATA HDD, and severel hundred GB in smaller Ultra ATA HDDs. I want to consolidate data, but again, want to save $$$. Would it be better to buy a couple $70 HDDs and put two in RAID-1 ? This is new to me. Also, I am interested in setting up a dual boot system. Windows XP/Vista and Ubuntu Linux. Or even triple boot with all three. Don't know the first thing about this.

Disk Drive http://www.newegg.com/product/product.asp?item=N82E1682...
Thats about it. I also have a floppy drive sitting around, though I don't know if it will work.

In summary, I am building a mid-range Gaming/Processing computer. (I am a physics major, hence the Linux and need for power to run Mathematica and other programs). I don't know whether to go Vista yet or stick with XP Pro, but I would like to play Bioshock at a nice graphics level. I need to know about modern HDD setups, and the general advice. My old machine could make it another year, although games like Medieval 2 run choppy in large battles, even on low graphics. I also don't know the first thing about overclocking, just that it is good. I checked the compatibilities, but I have been known to err. Did I forget something? Help please!