Eagle said:
Well motherboards with AGP can be a drain on your resources and slow your computer down, so if you dont need it some people choose not to have it. The same is true with ISA (yes they still exist) but they slow down your computer when they are enabled and while AGP usually can be disabled, ISA usually cannot. I'm not sure of this but even disabling the AGP slot may not be enough to free up your resources. I believe that is why they sell all PCI mobos.
1. Wrong (partially)
2. Completely wrong.
1. AGP slot itself is only a fast PCI slot with some advantages and disadvantages.
Good it fast for video card (writing to card)
Bad - even if you make hdd controller for AGP slot it will be slow as hell because AGP is a bit one way bus - writing to device is fast but reading from it is slower than PCI
What makes such slowdowns on computers with 128 or less RAM and AGP cards with AGP enabled in DirectX settings - DiME (Direct in Memory Execution) Card is trying to fit textures to computer's main RAM and even trying to work with them directly in RAM...
But there's already not too much RAM so disk swapping is begun...
And even if there's enough ram so no HDD access - on older PC's RAM
is slower than video card's VRAM and you need to access it through AGP then system bus, long and slow way...
That's why cheap onboard video is always so sloooooooooooooow - they don't have VRAM, only shared computer RAM.
And if you disable AGP in DirectX it will not disable AGP bus but will refuse DiME and force PCI-like mode which is good if you have enough VRAM and don't want to slow your computer down.
Voodoo 3-5 video card don't use DiME (thy are just a bit faster versions of PCI cards) so there's no swapping with them.
Older Nvidia cards like TNT or GF1 have bug with DiME - they trying to use RAM even if there's enough video memory.
DiME is not too good feature - if you don't have enough VRAM playing game with 8-12 fps is not much better...
Thats why professional cards come with 384 or more megs of video memory...
2. ISA is a bit slow bus but itself it not causes any slowdown.
only if you use antique cards not capable to do DMA thing

Unlike USB which always drains some resources...
Main "brakes" in modern (home) computers is "economy features" such as softmodems, CNR or onboard software network cards, AC'97 (codec-only) sound, AGP texturing aka DiME.