Although I'm not aware of a standard that would specify that, the best practice I know of is to keep all fibers INSIDE the patch panels in their original order (Here is a reference) and perform any crossovers with patch cords. You will have to install at least one cross-over fiber cable per link. The easiest way of doing the cross-over on fiber is to use one of the cords with SC or LC connectors NOT clipped together, at least on one side. This way you can easily swap the fibers in a GBIC. If you are using ST connectors by any chance, they are never clipped together, so you are free to make ANY cord either straight-through or cross-over, depending on how you connect it.
Remember to cross-over the fibers on one end only. The link light on the GBIC is your best guide.
Dmitri Abaimov, RCDD