Laggy / slow system issues

My computer has been progressively getting more and more laggy when loading anything, this includes the loading of my O/S (Windows 7 Ultimate), opening folders / files, any program including very small programs such as Notepad, webpages with any level of data over just text, sometimes even full text webpages will open very slow. This problem has been getting progressively worse, and I am wondering if it might be because of hard drive failure. I have rebuilt my system several times now, 3 to be exact, and each of those times have used the same hard drive, this has probably been over the coarse of the last 6 or so years. All the other components have been replaced with the exception of the case. I am very diligent about keeping my computer clean (software and hardware wise) and run glary utilities and CCleaner on a weekly basis, this use to have some effect in making the system run better, but has since stop showing any performance boost. I have two hard drives in my system, though I do not run the drives in RAID or anything like that, one is used for my O/S's (I dual boot Windows 7 and Ubuntu ) and the other is used for storage of media. I have run multiple disk check software on the hard drives and everything checks out as normal. I ran a Windows repair on the system and always made sure my OS is completely up to date, I seem to have this lagging issue when booted into my Ubuntu OS as well, so I do not think it is a operating system problem, but I can do a complete reload of my Windows OS if that sounds like it is actually the issue. Just trying to avoid it. Also just to rule it out, I ran a speed test on my current internet, and am receiving 12.8Mbps download, but only .05Mbps upload and I am wondering if that is something to do with my hard drive not being able to send data as it should be, my ping was 21ms, this was read off Speedtest.net. I have tested my network on other devices and am getting around 1 -3Mbps upload on those. Currently my system has the following components installed -

Motherboard - ASUS P6T Deluxe V2 LGA 1366 Intel X58 ATX Intel Motherboard
Video Card - NVIDIA GeForce GTX 260
CPU - Intel Core i7 CPU 920 @ 2.67GHz ( No overclocking)
RAM - 6GB
Hard Drives - 2x 640GB WD 7200RPM
PSU - 750W Corsair

If you need any more information please let me know, would love to figure out exactly what needs to be done so I can get my system back up to operational capacity. Any help would be greatly appreciated, thanks a bunch in advance.