Yes, Superfetch will probably help over time, and you should give it a dozen or so boots to optimize itself. But there are all sorts of things that can happen between login and the desktop that can hang things up, and most of them are only incidental to HD speed. So if the benchmark programs listed earlier don't show anything amiss with your disk hardware and configuration (PIO vs DMA mode, etc), you'll want to look into what you've got running at startup (background apps, services, "drivers" for all-in-one printers or optical drives, other 3rd party bloatware). You also might be encountering a hang due to network log-ins, unreachable network drive shares that Windows is trying to reconnect, etc.
I feel like my new WD 1TB HDD is slower than the HDDs on my Toshiba laptop that I got over 4 years ago. And it's supposed to be SATA 6Gb/s. Is there any way to test if the HDD is functioning in full capability?
I'm not sure if you meant it that way,but you realize that the SATA standard isn't going to make any perceptible difference with an HD (bursts from cache might be faster, but that has a trivial effect; the actual transfer rate from the HD wasn't going to saturate 3Gb/s SATA either)