culled from
'Optimizing Windows for Games, Graphics and Multimedia'
by David L. Farquhar, O'Reilly (http://www.oreilly.com/catalog/win9x/)

"The Windows registry grows as data is added to it, but it never shrinks when 
data is removed. A bloated registry with a lot of empty space in it can slow 
down boot time as well as Windows performance as a whole. All three major 
Windows utilities suites--Mijenix's Fix-it 99, Symantec's Norton Utilities 4.0, 
and Network Associates' McAfee Nuts and Bolts 98--have registry compaction 
tools. Note that Microsoft's popular RegClean tool does not eliminate empty 
space from the registry--it just removes invalid keys. This, too, can speed up 
the boot process slightly, but those invalid keys become empty space after 
RegClean removes them. To reap the full benefits of RegClean, you have to 
compact the registry aswell.

If you don't have any of the major utilities suites, you can still compact your 
registry with a few commands from MS-DOS mode. Note that these commands MUST be 
entered from MS-DOS mode--they will not work properly from within Windows. 
Before you enter these commands, be sure to Start -> Shut down -> Restart the 
computer in MS-DOS mode.

RCOMPACT.BAT:
------------
md c:\windows\backup
del c:\windows\backup\registry.reg
del c:\windows\backup\system.dat
del c:\windows\backup\user.dat
regedit /e c:\windows\backup\registry.reg
attrib -r -s -h c:\windows\system.dat
attrib -r -s -h c:\windows\user.dat
move c:\windows\system.dat c:\windows\backup
move c:\windows\user.dat c:\windows\backup
regedit /c c:\windows\backup\registry.reg

These commands make a backup copy of your registry in C:\Windows\Backup before 
they pack it. If an old backup exists, it is deleted. If the directory 
C:\Windows\Backup doesn't exist, it is created. Be patient, as these commands 
take some time to execute.

Should the process fail and your system lose its ability to start Windows, boot 
into DOS mode and issue these commands, which will back up the bad registry and 
replace it with the backup copy that the previous commands just made:

RRESTORE.BAT:
------------
attrib -r -s -h c:\windows\system.dat
attrib -r -s -h c:\windows\user.dat
ren c:\windows\system.dat c:\windows\system.bad
ren c:\windows\user.dat c:\windows\user.bad
move c:\windows\system.bad c:\windows\backup
move c:\windows\user.bad c:\windows\backup
move c:\windows\backup\system.dat c:\windows
move c:\windows\backup\user.dat c:\windows
attrib +r +s +h c:\windows\system.dat
attrib +r +s +h c:\windows\user.dat"