Sorry - I glossed over the bit about the download cache.
The MMC snap-in is installed with the .NET runtime - however, it doesn't
really provide any capabilities over the shell viewer that I know of.
Specifically, it doesn't seem to do anything with the download cache.
If you still want to take a look at it, you can get to it from the Start
Programs\Administrative Tools\Microsoft .NET Framework 1.1 Configuration
If you want to write your own utility, the path to the download cache is
%USERPROFILE%\Local Settings\Application Data\fusioncache.dat
I don't know where you'd find this file on Win 9x machines that don't
have user profiles set up.
Deleting everything in the directory specified in that file seems to do
the trick on my machine.