There are many benefits from Multi-core processers.
Whilst there is not a huge amount of software that actively makes use of both cores (I know 7z is multithreaded, and compressing is a huge amount faster than on my old single core chip) multitasking brings these chips into there own.
I would love to see someone with a pure single core (hence excluding P4 Hyperthreading) try to easily cope with general computer use whilst running a virus scan or anything else cpu intensive, guaranteed. Also try playing a fairly old game (just to give it a chance) ie UT99, whilst converting MP3's to WMA's.
Once quadcore comes along this will occur even more, cores sharing out processes between them.
Handling multiple processes is not as complex as you seem to think, the process is just given to the least active core.... that was complicated wasn't it
btw, I am writing this message whilst doing a full system virus scan with AVG plus a spyware scan with Adaware. Meanwhile my computer is still pretty resposive considering both cores are under constant use, my music isn't even stuttering
oh and ps, all the affintys are set automatically