The 10.4.9 update's "feature" of boosting built-in speaker output on various Macs came with mixed reviews. I'm one of the ones who thinks the lowest GUI-accessible setting is now too loud.
Quite by accident, I discovered that turning down the volume all the way, then muting and unmuting the speakers via the keyboard gives me the quiet sound I've been missing.
[robg adds: This is the first I've heard of a volume boost in 10.4.9; my MacBookPro seems the same now as it was before, so I'm curious about it. If anyone knows more, please post in the comments -- which models did this supposedly affect, for instance?]
Mac OS X Hints
http://hints.macworld.com/article.php?story=2007042221445186