For pesticides, many manufacturers offer recommended pairing for pesticide confirmation.
For environmental work, (and running pesticides in what sounds like natural products would be fairly related) the problem is that on any given sample when we're running a long list of analytes, the likelihood of having something extract that has the same retention time as our target analytes approaches 100%. Its from this issue that a lot of the USEPA methods require that for GC work we confirm any positive detect with a column of dissimilar phase.
As Rod states, what you need to do is select a column with significant differences in polarity (while still chromatographing the compound). It may be easier to think about this in terms of what wouldn't be a good choice. For instance the common DB-1 is a methylsilicone based stationary phase, and a DB-5 is a 5% phenyl, methylsilicone phase column. Though there is a slight difference in polarity, for all practical purposes the separation between these two columns is very, very similar. Now, USEPA method 507 uses a DB-5 for primary and a DB-1701 for confirming. The DB-1701 is a 14%-Cyanopropyl-phenyl)- methylpolysiloxane phase; which is fairly more polar than the 5% phenyl methyl silicone column. Most column manufacturers have come out with proprietary columns for pesticides which tend to work a lot better than what was originally referenced in the USEPA methods, but because they are proprietary, the manufacturers don't give us much in the way of column information.
In any case, what we're attempting to do is select columns with significantly different stationary phases so that we have a higher level of certainty in our measurements. When we review the manufacturers, the more info we have regarding their polarity the better you can make these determinations.