Basically it's a way for developers to differentiate different internal builds of Mac OS X released to them. Sometimes Apple creates nightly builds, so they need a way to keep the versions separate as well as a way to show how much work has been done on each version.
To the end user, the build numbers usually don't mean much. But to the developer, sometimes it's very important to know if you're using build 5Q25 of OS X 10.1.3 or 5Q45 of OS X 10.1.3, and it might help Apple support, too.
You can also see how much work has been put in based on the build number. After the April 2002 Security Update, the build number went from 5Q25 to 5Q45 (I think), so you can see that there's a bit of change in there. In contrast, OS X 10.2 is up to 6C35 or something, and you can see that there is much more work gone into these builds because the build number starts with a 6 instead of 5.
I don't think it's anything beyond this. The letters don't mean anything specific it's just a different naming scheme.