12 VDC with non critical voltages for running the pumps and fans. Use diodes. The fans, and pumps will see 11 VDC, but will still run, but likely a bit slower. The diodes can be mounted to a plate of aluminum to heat sink them, but isolate them from the heat sink if they have cases that are live.
As for connecting the grounds. Because of the isolation in the power supplies, that is a non issue unless the site has badly messed up wiring with power from two transformers going to the same outlet and don't have properly earth grounds. Even then they likely share an earth ground so it is still a non issue.
My question is with the third power supply. What happens if the third power supply doesn't come on, or fails during use? Can your system automatically deal with that without cooking a CPU? Both the diode and relay methods allow the fans to continue to be powered with a power supply failure. Diodes have the advantage of being more reliable, but the disadvantage of the voltage drop. Relays can have contacts weld. Even at 12 VDC.