Are you sure it's the Hard Disk and not the processor? It is true the Hard Disk tends to be the biggest bottleneck in modern computers, but it is the processor maxing out at 100% usage (or nearly so) that generally counts for that dead-in-the-water feeling you can have with some computers from time to time.
Logging processor usage can be done with the CPU Utilization Monitor (or I assume any number of other apps, this was just the first FOSS app that showed on a google search for "log processor usage"). The app states that it's logs can be easily viewed in Excel for analysis and reporting.
UPDATE now that I've used the CPU log app:
The package you'll download for the CPU Utilization Monitor includes programming files that you won't need. But in the /bin/ directory you'll find the compiled executable (the program all ready for you to run).
It's a pretty simple interface that will show you visually what your current CPU % utilization is and then a series of bars that indicate the percentage of time your CPU has spent at any given percentage level of usage. There's also a place to choose where this data is being logged. Pretty simple and self-explanatory. Does one thing and does it well enough.
Make sure to check both Calc Moving Average and Log Moving Average to actually save the data to the log.
UPDATE with Hard Drive logging option:
Since you're certain it's an HDD issue, the standard rule applies: Make sure the drive is defragmented.
I'm assuming you have Win7 or Vista, which should both automatically defrag your disk at regular intervals, but at least check and make sure this is occuring.
Next, because ResMon and PerfMon are tied into the system you can using built-in Windows tools to log events. They won't necessary report to you the percentage of the time the HDD is pegged at 100%, but you could probably set the rules to record an event each time HDD usage goes above 80% and possibly record how long it stays there.
I don't have a Vista/7 box to test this on myself right now, but here's an article from Technet that details how you may do this logging using the windows tool logman: How to pull the information that Resource Monitor provides.