Long story short, I bought a new second HDD, and while installing it I decided to reconfigure the way my drives were connected. In doing so, the HDDs ended up on the other IDE channel (I swapped the plugs over). I noticed a massive slowdown in my PC and measured it with some benchmark software. After putting the HDDs back on the secondary IDE channel the PC went back to normal (fast). Don't ask me why this is the case - I've checked the BIOS settings.
So, if you know what you're doing you mighht want to try swapping your IDE cables over ;)
So, if you know what you're doing you mighht want to try swapping your IDE cables over ;)