Good question although one that keeps coming up...maybe we should add it to a FAQ. I suggest listing the TX ERP when you search. The repeater usually has higher power than the other stations listed, which use the reverse TX-RX.
Of course, you could always try both (unless it is a large system). Another clue is that in the UHF bands, the repeater is usually the lower of the two, usually 5MHz apart (but not necessarily, there are exceptions). For example, repeater output is 451.2875, input is 456.2875. In the 850 bands, the repeaters are 851-869, and their inputs are 806-824.
Is there a specific instance you'd want us to look at?
Dave