Thanks for the replies guys.
It is a desktop PC and my main drive is an SSD, so performance of my storage drive doesn't need to be to of the line. Also, as @mta noted, the performance of WD Green drives is actually pretty good.
Anyway, this is all besides the point. As I stated in my original post - the defrag speed was much quicker using a different defrag program, it ended up doing more in 1 hour than Defraggler did in 8 hours. This points to an issue with Defraggler and not my hard drive. It seems as though for whatever reason, Defaggler would only use 30% of my hard drive's transfer capacity, while the other defrag solution used 100%.
Could it be a compatibility problem with something else I have installed or with Windows 8.1?