The version you get from Software Update is the same as the one from
http://www.apple.com/downloads/macosx/apple/macosxupdate1043.html. It updates from 10.4.2 to 10.4.3 only.
The combo updater from
http://www.apple.com/downloads/macosx/apple/macosxupdate1043combo.html, as stated above, updates from 10.4, 10.4.1 or 10.4.2.
I get try to get the Combo for several reasons:
1. In earlier versions of 10.*, the combo resulted in less issues than serial step updates. Often running the appropriate combo would clear up issues resulting from serial updates (much on macosxhint forums on this).
2. I download the system updates, using Sofware Update as more of an indicator, because I have multiple machines to update.
3. If I have to rebuild an OS, the combo (past update *.1) makes it a single step. For example, imagine rebuilding 10.3.9 serially -
NINE steps!!! The multiple machines just magnify this issue.
Maybe this is just a case of serendipitous old habits dying hard but my update process is to repair permissions before and after running MacJanitor and then run the appropriate combo. Since I developed this, er, habit I have not had a single issue updating the OS....
YMMV...