40 GB as a system drive is quite small, have you ran the disk cleanup wizard by going to my computer> right click on the C:/ and then properties> general> disk cleanup
It scans for dump files, temp files etc and then gives you the option to remove them, I have seen this clear over 8GB of space in older systems...
Let us know how you get on.
The other thing you could do is install any games that you want onto the secondary drive, as the system is quite old you shouldnt see any major performance loss by having the files on the other disk.