In reply to Chip Bennett.

You're talking about several different things here, all of which may be handled similarly or differently:

1) Social network profile links
2) Social content-sharing buttons
3) Header/footer scripts

There is an argument to be made that social content sharing links in a Plugin may not be able to be as tightly integrated into a Theme's design, but there are alternatives: make the Plugin output overrideable via CSS, implement standard template hooks (such as the Theme Hooks Alliance) to allow the Theme developer control over where the links are displayed, etc.

But for header/footer scripts: those belong in a Plugin. That's what I'm talking about when I say that I can't think of a valid argument for having them in a Theme.