I was running Software Update on a fresh install of 10.3 tonight, and I thought to myself ... instead of minimizing Software Update while it is running to speed it up, why not just fix the problem?
It turns out someone already figured out how to do so, but for a different application. After searching the archives, I found this hint for Camino. To do the same for Software Update, just edit /System -> Library -> CoresServices -> Software Update > Resources > English.lproj -> SUAppWindow.nib, and do as instructed in the prior hint. Now everything is as fast as it is minimized, but I get to watch it work.
[robg adds: I don't notice any drag on my machine, but this should make a difference on slower machines. This hint is a more automatic fix for the general problem noted in this hint, where GUI updates take so much CPU that they slow the process of the operation. The temporary fix, as noted, is to hide or minimize that application's window. You should back up the application first, just in case, and note that future software updates may update Software Update, thereby removing the fix :).]
Mac OS X Hints
http://hints.macworld.com/article.php?story=20041127201819612