I currently have both ATA channels full on my motherboard (DVD and a CD writer on one, plus my 40/80 gig HDs on another). If I buy a PCI controller card, will I still get ATA 100 transfer speeds, or are the transfer speeds limited to the speed of the PCI bus?
The speed of the PCI IDE-controller decides how fast your HD's can run. With a 133-card you can run ATA-133/100/66/33 HD's.
Note that the lowest speed of a pair of HD's (say 133 and 100) is the one that will be maintained (in my example both HDs will run at 100).
Something to seriously consider is a more powerful Powersupply. Go for 430 or higher wattage and buy a brand-name like Enermax or Antec etc.