There are at least three different arduino bootloaders in COMMON use.
ATmegaBoot is compatible with mega8, mega168, mega328, and mega1280, at least.
OptiBoot is compatible with mega8, mega88, mega168, mega328, mega1280, mega644, mega1284, and some others.
stk500v2 is compatible with mega1280 and mega2560, and probably others.
Note that these are source-level compatibilities, possibly requiring that you compile the bootloader yourself.
A particular .hex file is essentially only good for a single processor.
I had meant via the "Burn Bootloader to Arduino" option in the IDE, but I guess I never considered the fact that are others floating out there... Which one of the above is used in the IDE? Sorry, I know this is kind of a noob question... :\ Might as well learn about it now though.