When I built my current system (i5-2550k, Gigabyte GA-Z68XP-UD3 motherboard), I decided to go in an unusual direction. I purchased a Kingston SSDnow mSATA 64GB drive, which went into the mSATA slot on the Gigabyte board. I also had a SanDisk Ultra 120GB SSD, which became the 2nd drive in the system. The Kingston has just the OS installed on it, and the SanDisk has just program files installed.
Now, I'll state that with this arrangement, the boot times and access times are definitely an improvement over the old boot drive (which is now the E: drive, a 600GB Velociraptor). I do have to remember that programs installed have to go onto the D: drive, but I've managed to keep the drive space usage fairly reasonable. Right now I have 34.7GB free on the Kingston, and 81.6GB free on the SanDisk (that includes a full install of Office 2007 as well as the complete install of Adobe CS5 Production Premium). Combined with 16GB of onboard memory, the system is definitely overdesigned for what I use it for, and probably will remain so for at least another year or two.