You could create a folder on your drive for your downloads and then check the files over for viruses before running them. At the present time you have a lot of spare drive space - if you want to keep the used space to a minimum and you have a CD/DVD burner you could transfer the files to CD for storage and then delete the downloaded files.
Having a substantial amount of data on your drive shouldn't make any major difference to the speed things work at - it will help to defrag your drive regularly if you are downloading and deleting a lot of stuff - go to My Computer again and right click on the relevant hard-drive (local drive icon) select 'properties' then 'tools' and you will see the 'defrag option'. It can take a while (depends on the size of the drive, how much data, and what state it is in), so leaving it running last thing at night can be quite a good idea.
The other thing I find keeps everything moving at a good pace is to run Regseeker about once a month to clean out any unwanted stuff that's hanging around in the registry. Be sure to check the back-up option and if you run it on auto :'clean the registry' you can use your delete key to remove the unwanted bits and pieces.
http://www.snapfiles.com/get/regseeker.html
You can also use Regseeker to manually remove individual keys but unless you are absolutely sure of what you are doing this can be very risky and lead to problems starting or running your machine - so be careful on that issue.
If your machine suddenly slows without explanation, the first thing to do is to check for infection and Trend Micro Housecall is a very good way of getting an independent scan to double check your resident anti-virus protection.
I have found the Microsoft Anti-Spyware program to be pretty good too - it's free and runs in the background with automatic updates.
Peter