When I click the big download button at GitHub, I don't know what version I'm getting. On the download panel, there are three additional versions listed for download. Which is the most recent, the default or 3.0.0.3?
And does the big download button get me everything for that version?
On GitHub, when you click the "Download" button (not the tab), you will download the latest revision (known as the master branch in Git) in the repository. This is potentially untested code and should be avoided in production environments.
To answer your question specifically, you should download 3.0.0.3 unless you want potentially untested, beta-quality code.
For more reliable information, check the SubSonic Download page.