the Apple Remote always behaves the same and always consumes the same 
amount of power, regardless of whether:

- your Mac is turned on or off 
- which software you use on your Mac 
- you point it to a rock, a computer or anyhing else

The Apple Remote is rather dumb: it only sends signals, but can't and 
never does receive any.

Thus, whether you run Remote Buddy on your Mac or not is totally 
irrelevant to the lifespan of your Apple Remote batteries (you may, of 
course, use your Apple Remote more frequently with Remote Buddy).

If your batteries run empty in 2 days, either your Apple Remote is 
defective or the batteries you use with it are not fresh or of the 
wrong kind.

I'm still using the Apple Remote I received with my iMac in January 
2006 with the battery it shipped with. And, sure enough, I'm a power 
user ;-)

Best regards, 
Felix