Just so that everyone is clear: I don't plan to package the plugins themselves with the themes, just the hooks. The ones I'm most interested in are ones that would require the user to open their template and make a change. My purpose is to, as Skippy put it, to ensure that "the inclusion of (proper!) support for the plugins in the theme itself will go a long way toward helping new users hit the ground running."
Take the first four items in the list:
# Uber Tooltips Replacer
# Comment QuickTags
# Edit Comments
The first one is failry automatic, but I'll include some styling in for it in the CSS. The next three actualy need a coding change in the template file itself. These are the ones that have things like "if (function_exists("getWhatsPlaying"))" surrounding them. Things that are PnG (Plugin and Go) like the Permalink Redirect don't affect the template. (although I may employ that plugin in my own site.) So, while it's good to know about them, theme editing is the primary criteria for "making the cut" onto the list.
But, it is good to see what others are using, there's a bunch of good stuff out there I never knew about.
Keep 'em comming.