In iTunes, you can see the charge status of the iPhone currently connected:
This updates as the phone charges, and even shows when the phone is done charging.
Is there a way I can discover the charge status programmatically from the Mac? Any programming language or API is fine.
As far as I know, the only official way to communicate with the iPhone over USB/Bluetooth is by signing up to the "Made for iPhone" program:
http://developer.apple.com/programs/mfi/
Unfortunately the documentation seems to be closed to registered members so I can't find out if the API for this is public or private. You could contact Apple to check before applying.
UPDATE : As mentioned, this might not work for Mac/PC <-> iPhone communication over USB. There are several apps that do things with the phone over USB (although usually for reading/writing files). I'd start by looking at the source code of those:
http://code.google.com/p/iphonedisk
This should put you at least in a position where you have a connection to the device and are able to send/receive commands. Everyone who's ever done this sort of thing has had to spend time reverse engineering the thing :) The jailbreak community might be able to provide some insight too, although having to actually jailbreak the device is probably unacceptable.