My AUTOEXEC.BAT has this lines:
@IF NOT EXIST C:\WINDOWS\TMPDELIS.BAT DELTREE/Y C:\WINDOWS\TEMP\*.*>NUL
@DELTREE/Y C:\WINDOWS\TEMPOR~1\CONTENT.IE5\*.*>NUL
@DELTREE/Y C:\WINDOWS\COOKIES\*.TXT>NUL
@DELTREE/Y C:\WINDOWS\HISTORY\HISTORY.IE5\*.*>NUL
TMPDELIS.BAT is a batch file created by many installation programs that tells the system to delete whatever dross remains from the installation on reboot.
The first nukes the contents of C:\WINDOWS\TEMP 
only if that file is not present.  The rest of these clears up a lot of garbage that builds up in IE.  Don't worry about the subdirectories under these directories.  Windows rebuilds them on reboot.
The redirect, 
>NUL, just tells the sytem not to bother telling me about it.   
