As we wait on the threshold of 10.6.3, there are still some hiccups and interesting issues in Snow Leopard that might make your life a bit more difficult (as Aron mentioned recently). In particular, getting your Apple Remote to behave properly with all the apps that it's supposed to control may be an exercise in frustration.
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.