what version of windows are you running? the version 9x/Me or 2k/XP will tell us a lot in how to help you.
One of hte best ways, regardless of OS version, is to boot into safe mode, find EVERY temp folder you have in every directory if possible, and delete everything inside of them. Even hidden temp folders (like in Docs&Settings/Local Settings/Temp) in windows 2k/XP. ESPECIALLY make sure to clear out all the temps from the java folders wherever they be at on your system (this is how i get most of my problems, is i run with java on, and most problems with trojans/viruses i ever get are from java-scripts.