Going by your description I think you have temperature sensors that are distributed over some area in a room - maybe a few feet or more - and you have to regulate the temperature of these distributed "boxes" by a PC / MCU / Both.

In all such cases, much will depend on the kind of signal conditioning and whether you have them near the sensor ( preferred ) or you have them near the PC away from the sensor ( possibility of noise pickup ). In my opinion this should guide the layout more than the +5 and +12 available in the PC.

I am not sure what leeway you have in deciding the hardware but this would be one way :

1. Powered signal conditioners near each "box" with sensor.

2.Amplified, Differential analog temperature signal fed to a multi channel ADC + MCU combination.

3. Being an 80386 PC, a serial link to the PC from the MCU is preferred.

4. Scan the Temperature channels once per 500mSec or so ( temperature values dont change very fast normally )and with the dedicated control algorithm running on the PC ( maybe C / Basic )control the pumps with maybe a parallel interface card.

If you have access to a ISA /PCI based multifunction card, then the steps from point 2 above will be much simpler and you dont even need a MCU+ADC.

Raghu