Biggest bottleneck I see is the hard drive. But that's typical for most systems. However your is a green drive, which is more focussed on saving energy.
I suggest you check out an SSD, preferrably from OCZ or Intel. I like the Vertex II 100 or 120 GB in the $200 range.
If you are absolutely opposed to the idea, then there is a samsung 2TB on newegg that is here for $80:
Whenever you have a computer, there's going to be at least one part in it that bottlenecks the rest of the system. That's just the way it goes.
I would agree that the slowest component you have is the hard drive, followed by your Video card.