Thanks very much for all of the replies.
I have installed and run Jperf. With the default settings I got 50-55 MB/s, I then (as suggested) ran it again with the "TCP Window Size" set to 64 Kb, and got a respectable 108MB/s which is exactly what I was hoping for.
Next thing to look at is Write speed for my HDD's.
For this I will test the write speed (on my server) from one of my single drives to the other. I selected 10.1 GB of large files and copied them in one go to a 2TB Samsung 2TB HD203WI which measured a very disappointing 68MB/s
Both of these drives are wired up to my Highpoint RocketRAID 2320.
For my next test I copied 10.1GB (different file set) from my RAID-5 array (because is 99% + full) to one of my single drives and got 75MB/s. Also very disappointing.
I have re-read (skimmed) some review of my RAID card to see what kind of performance other people got, for single drives doing simple "large" file copy tests they exceeded 100MB/s, sadly the rest of the tests were far less clear about the "write" performance, especially in RAID-5.
Another test result for you, when I read data from my SSD in my desktop to a single drive on my server I get 68 MB/s, which rules out the issue of the RAID cards internal bandwidth being a limiting factor.
Another test involved me torturing HDD's. I copied the same 10.1GB data set from a single drives to my RAID-5 array which had just 13GB of spare space (2.91GB at the end) - the result is only surprising because of how fast it was, 61.5 MB/s.
I have just one last test to try, testing the boot drive. This is an ancient 400GB Samsung HD400LJ, and as this drive is also 99% full I am copying data from that drive on my server onto my SSD in my desktop, for this result I got MB/s.
So the results as I see it point towards my RAID cards write speed regardless of whether its a single drive or my RAID-5 array.
A couple more things to note:
I am running 2003 server, and was planning on doing a re-install with a desktop version of Ubuntu (exact Linux version may vary, driver support needs to be factored in and I want a GUI) when I add 4x WD Red drives to my RAID card as a RAID-5 array.
HD Tach gives an (average across the entire drive) read speed of 90.6 MB/s (high of 125 MB/s low of 45 MB/s), whilst the RAID array gets 264.5 MB/s (high 310 MB/s, low 190 MB/s), an important thing to remember is that a RAID-5 array will by its nature always have a much faster read speed than write speed, by a single drives read and write speed are very similar (providing there is a decent amount of spare space - 560GB in this instance).
I have also noticed a trend, every single data transfer starts of with a reported speed of 100MB/s or more, I can only assume this is a result of caching.
The one thing that I have learned from all of this, is that my CPU is not an issue.