The advantage of the Omnifuel is that it has a valve at the burner which allows for simmering. The advantage of the Whisperlite is that it's less expensive, quieter, and lighter.

I haven't spent a lot of time scouring the lines of any of my MSR stoves, but I usually do a flip stop which purges the line. See the fourth video down on my blog for a demonstration of the flip stop. If you've got an Omnifuel, I imagine that you already know what I'm talking about.

HJ