I checked my hard drive with Western Digital's diagnostics tool, but I didn't run the advanced test (check for bad sectors) and it passed. Also, when copying large amounts of data (200-400 MiB files) from my S-ATA drive to an external USB, I get 50-60 MiB/s, which is what I usually would get (i.e. limits of USB2).
The problem is when several programs use the hard drive, which is when it goes down to 3-4 MiB/s. Could this maybe have something to do with bad head seeking?
@shovenose: thanks for the tip!