Defrag your hard drive. The files are slowing you down because your hard drive is thrashing and chugging trying to find things. Think of it as a file cabinet. The more organized, the faster you can find things. The games themselves are just files on your hard drive until you run a program, if they aren't loaded into memory they won't affect performance. It might be a good idea to also check and see what programs are loaded into memory when Windows starts. Some startup programs can cripple performance by eating up all your ram.
if that is a frequent problem, drop in more ram if you have some free slots.