One 500GB drive divided into two equally-sized partitions. The system drive (C:) has 50GB free, while the D: drive has just 47MB (yes, that is MB) free - that couldn't cause slow running could it?
Machine is a Dell Dimension E520 desktop computer running Vista Home Basic/Premium (currently defragging and don't want to interupt it to confirm).
It has McAfee Internet Security (AV, Firewall and spyware) installed and active so I scanned with that and found nothing. Ran Malwarebytes Antimalware and found 119 infected objects, amongst which were a couple of trojans, all of which it got rid of. Disabled McAfee, downloaded Microsoft Security Essentials and it found and removed two JavaExploits.
Ran CCleaner (just the cleaner - not brave enough to run the registry cleaner side of it as I've heard of it causing problems) and it got rid of about 5GB of temp files and stuff.
It's currently running Piriform's Defraggler but I'm not hopeful (1) because it was only 14% fragmented, and (2) even after running all the other stuff (but before running Defraggler) it was still like running through treacle when trying to do anything. For instance, the Malwarebytes scan took over 5 hours to scan the C: drive; Microsoft Security Essentials took 4 hours, Defraggler has currently been running for about an hour and a half and is 27% completed.
What else can cause slow running?