After reading your topic, I just tried Software update on my iBook G4 running 10..3.9 and also find Software Update no longer functions.
SoftwareUpdateCheck[347] connection:didFailWithError: timed out
SoftwareUpdateCheck: network error
Whilst I don't have any officail list of 10.3.9 updates, I can post My Software update log for you.
The dates are when I installed the updates, not the date of the update issued, but you would know that.
Software update log
2005-07-09 22:14:01 +1000: Installed "Battery Update" (1.1)
2005-07-10 11:38:46 +1000: Installed "Mac OS X Update Combined" (10.3.9)
2005-07-10 14:52:03 +1000: Installed "Apple Remote Desktop Client" (1.2.4)
2005-07-10 14:52:13 +1000: Installed "iPhoto Update" (2.0.1)
2005-07-10 14:52:30 +1000: Installed "Java 1.4.2 Update 2" (1.4.2 Update 2)
2005-07-10 14:53:19 +1000: Installed "iCal" (1.5.5)
2005-07-10 14:53:26 +1000: Installed "Java Update for Mac OS X v10.3.9" (1.0)
2005-07-10 14:53:35 +1000: Installed "Security Update 2005-005" (1.0)
2005-07-10 14:53:44 +1000: Installed "Security Update 2005-006" (1.0)
2005-11-12 13:34:50 +1100: Installed "Security Update 2004-10-27" (1.0)
2006-01-14 11:32:00 +1100: Installed "Java Security Update" (4.0)
2006-01-14 11:41:00 +1100: Installed "Safari Update" (1.3.1)
2006-01-14 11:56:00 +1100: Installed "Security Update 2005-007" (1.0)
2006-01-14 12:10:00 +1100: Installed "Security Update 2005-008" (1.0)
2006-01-14 12:24:00 +1100: Installed "Security Update 2005-009" (1.0)
2006-01-14 12:36:00 +1100: Installed "Safari Update" (1.3.2)
2006-09-05 11:00:00 +1000: Installed "Security Update 2006-001 (PowerPC)" (1.0)
2006-09-05 11:10:00 +1000: Installed "Security Update 2006-002 (PowerPC)" (1.0)
2006-09-05 11:20:00 +1000: Installed "Security Update 2006-003 (PowerPC)" (1.0)
2006-09-05 14:03:01 +1000: Installed "Security Update 2006-004 (PowerPC)" (1.0)
2006-10-10 11:47:23 +1000: Installed "Security Update 2006-006 (PowerPC)" (1.0)
2007-02-18 11:47:23 +1000: Installed "Security Update 2007-002 (PowerPC)" (1.0)
2007-02-18 11:48:23 +1000: Installed "Security Update 2007-005 (PowerPC)" (1.0)
2007-06-02 00:58:14 +1000: Installed "Java for Mac OS X 10.3, Update 5" (5.0)
2007-06-02 01:31:43 +1000: Installed "QuickTime" (7.1.6)
2007-06-21 05:12:08 +1000: Installed "Security Update 2007-006 (PowerPC)" (1.0)
2007-07-25 05:12:08 +1000: Installed "Security Update 2007-007 (PowerPC)" (1.0)
2007-09-20 05:12:08 +1000: Installed "Security Update 2007-008 (PowerPC)" (1.0)
2008-12-31 12:06:01 +1100: Installed "Security Update (QuickTime 7.1.6)" (1.0)
2010-03-15 19:44:39 +1100: Installed "Xcode Update" (1.1)
All the best