Is there any way (e.g. with the command-line) I can upload an APK to an android phone wirelessly (wifi or Bluetooth) and launch it on the phone from a desktop machine?
I can do this things with abd from the command line when a USB cable is attached but I'd like to know if I can do this without having to mess around with cables.
The short answer is "no"... you have this nice new Bluetooth-enabled "smart"phone that doesn't do as much as the Nokia 3650 I had 8 years ago did (can you tell how annoyed by Android's lack of functioning Bluetooth in Android?).
The long answer is that the only way you could do anything like this right now would be to email yourself the APK then using something like APKatcher to install it. Note that this will not let you do any debugging, auto-install/launching, etc. It's a hack, at best.
I did this with dropbox, had my .apk installed within minutes on my phone. Just add the apk to you dropbox folder, install a dropbox app from the market and open the apk-file on you phone.