Hi Assay Queen,
There are a lot of ways to determine cutoffs, but it really depends on what you are trying to do. Can you be more specific when you are "setting cuttofs from a data set"?
At any rate, some standard favorites for determining statistical measures are:
Student's t-test.
Wilcoxon test.
If you want to get really hard core into cutoffs you can start thinking about using Bayesian techniques, clustering algorithms or even defining support vectors. But my guess is that you are probably looking for something much simpler, like one of the first two listed above.
Again, with sparse details in the original post, I'm not sure which one will apply to you, but hopefully that gets the wheels turning.