Here's the Idiot's Guide to PC Bottlenecks, Short Version. You can safely assume that due to the laws of physics and the engineering of the modern PC, this is it for application-agnostic bottlenecks.
Generic PC components, from slowest to fastest:
- Optical drive
- Network (wireless)
- Network (wired)
- USB-2, Firewire
- Hard drive (std, IDE)
- Network (wired, gigabit+)
- Hard drive (std, SATA-II)
- Hard drive (SSD)
- GPU, RAM, system bus
Now, any of them can be "the" bottleneck for a certain application or system configuration. If your application is slower than you think it should be, you have to consider everything about the PC to find the problem.
That's when benchmarks and measurements come into play, and things get complicated. Without knowing what application you're optimizing a PC build for, you can't optimize properly.
If all you want is to max out your hard drive speed, buy an SSD drive to go with whatever CPU/RAM/motherboard combination you decide on.