I don't know of one that handles everything you listed, especially the extenions, which are generally kernel extensions, as apposed to startup processes.
StartupItems is depreciated, and discouraged. Most likely used by some older apps to start a daemon.
You forgot cron which is an older Unix approach to running items as startup and on periodic schedules.
Lingon is a utility that deals with Launchd items.
Is there a current startup manager application for OS X?
Nope. It's a mess.
There are many places, several of them non-obvious, for startup items to exist on the Mac nowadays, and presumably any of them can cause conflicts, or at least console errors.
Here's the list I've compiled so far:/System/Library/Extensions/ (and don't say we shouldn't be messing with anything in there; I found a Virex extension in there yesterday!)You shouldn't be messing with anything in there. Nor should Virex. Usually this is a good indicator of a 3rd party developer that doesn't know what they are doing./System/Library/StartupItems//System/Library/LaunchAgents//System/Library/LaunchDaemons//System/Library/PreferencePanes/ (hopefully these are Apple-only, but who knows what some crazy software installer might do?)I know what they will do. I had one do both chown and chmod, sometimes with -R, on various / directories once. I didn't appreciate that. Why do we have the Mac App Store again?Is there any current software that handles this sort of thing?
Not that I know of. It sounds like an opportunity.