A possibility would be to give donators the ZPM tool. We did it on Drekens SB way back and it worked out really well. Non-donators had to create one with the generator or use a CAF fusion gen.
A second possibility would be to give donators a percentage based boost to core PG and CPU or something along those lines with the finite core resources.
Making certain CAP entities like Stargates and asgard transporters donator only.
Basically the objective is to find certain entities or tools that, from the point you spawn your ship, makes it more time consuming to get all your resources, or to make quick transport. (examples would be like making puddle jumpers donator only or as I said earlier, the ZPM's). Also making gas systems 3 donator only, GS3 makes everything much faster (almost instant).