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I wouldn't say that, nowdays soundcards, raid controllers, tv cards and nics are coming out in pci-e flavors. Nothing is limiting you to using the 2nd PCI-e slot to only a SLI/Crossfire setup.
I can only talk about sound cards and wireless cards (I don't pay attention to tv/raid cards) whilst there are 1 or 2 pci-e versions about (only sound cards I know are the Asus DX and D2X) the majority are still PCI based. I doubt we will see many cards going pci-e only in the next 2-3 years so you may as well go with PCI slots as currently it'll be easier to find hardware using a PCI card and I don't think it's going to be phased out for a while yet so it shouldn't be a problem in the life span of this build.
i have removed an sata disk while running, and put in another sata disk on that port, on my ich9r, it worked, however, i kept getting angry messages from libata untill i did insert the disk..
im wondering, is there anything one must do before pulling out disk? i googled for ~10 min but was unable to find any usable information.
make sure you have cleanly unmounted any filesystems on that device before removing it. That should help reduce the angry messages as before it seems the driver got angry you took the drive away from it without telling it
However there should be a way to tell the kernel you want to remove the device...
The nvidia 8800GT card was nothing the latest driver couldn't fix (although it is still listed as "unknown device" in lspci).
Try running "update-pciids" as root.. lspci uses a hardware database that is as up to date as when it was first packaged (which with ubuntu could be well before the hardware came out) running update-pciids will fix that.
A lot of "newbie" forum threads that claim lspci output as being evidence that "linux doesn't support most hardware" are easily fixed with update-pciids. lspci and hardware support are not really related (it will correctly list unsupported hardware too!)