Update: I'm going to close this off. It's too much hassle for me to update because I make so many changes, and it's not really all that useful either. You're better off looking at the code in the place you need a hook, and if there isn't one, add it to the SVN or ask a developer to do it.
Here is a list of plugin hooks. Expect this to grow as Hotaru does.
NOTE: For Hotaru to be as flexible as possible, it's important that plugin developers include hooks within their plugins. To help other developers, please post your plugin hooks in this thread. Thanks!
admin_header_include (called from the admin theme header.php template)
header_include (called from the default theme header.php template)