Luis,
I have often seen this, and I would start with checking two resources: free memory and free disk space. Check your memory when the machine seems slow, and see how much free memory you have.
The other trick is to run a disk-defrag, and see if this improves performance. A mostly full disk will fragment, and then the disk I/O slows quickly.
There are several other things, but those are the easy and user-friendly ones.
