I had a similar problem in the past, here's my two cents:
What worked for me (and what I've done for every other Windows install since then) is to install small groups of updates together. For example, install security updates in groups of 10. Also, don't install different types of updates together in one go - ie. .NET's go together, IE updates go together, security updates go together, etc. Further, I never install any of the IE updates until ALL other updates have been successfully installed. On a side note, I've had trouble with the ActiveX Killbits (I think that's what it's called) messing up my Windows installs and typically don't touch that until the very end (along with IE). Every time you restart your computer, remember to 'check for updates' before running the next set of updates as some that were previously listed may no longer be needed.
Hope this helps