Besides gear mesh and bolt pattern mesh - you need to consider application too.
Some PTOs are meant to drive winchs, some hydraulic pumps, some water pumps, etc.... the gearing inside them, as well as where they mount (tranny vs. tcase) are very specific. (output RPM difference)
For example - the SM465 PTO has to be "in gear" for the PTO to operate. Thats good and all as long as you can shift your tcase into neutral
when the application requries it.
On the flip side, having to have the tranny in gear to run a pump (water / hydraulic) wouldn't always be ideal.
Then to take it one step further - a PTO on your tcase would be worthless without the tranny in gear. Again, does the specific application you're currently in work with this scenario? You won't really know until you're there.
As far as winches go, electric is a whole lot easier to dear with, because all of the above don't apply.
(you can also mount some pumps off the engine drive pullies, again eleminating the complications above)