In the case of my unibody MacBook Pro, I couldn't get the machine to recognize any remote commands at all - even after verifying that the batteries were fresh (by looking for infrared flashes via the iSight camera) and trying to pair/unpair the remote. I wasn't alone; there's a five-page thread on Apple's discussion boards detailing a litany of woes with 10.6.x and remote use, with many reports of Front Row overriding remote commands destined for other apps like EyeTV.
Good news, though: even if the upcoming OS update doesn't clear up the remote issues, there's a fine & free solution right now. The Candelair driver, provided by the developers of Remote Buddy, installs simply and works like a charm. You can disable/enable the driver via the provided preference pane, or activate a legacy compatibility mode to help old apps behave as expected. For me, I'm just happy that my remote is working again.