It'll be fine, so long as the OS you're trying to run is later than the one that came with your system.
I do it all the time at work. I have an external drive split into 4 partitions. Three are for diagnostic programs, the fourth is an emergency OS I can use to boot any system if I need to verify something and the internal HDD is shot. And it's nothing special either.
So, say for example the laptop shipped with 10.5 (and it's an Intel based system) and your desktop shipped with 10.6. It would work just fine. If it's the other way around, you may have problems. My new 27" iMac requires 10.6.3 at a minimum, so if I tried using anything less it would kernel panic at boot.