ON the desk:
Pro:
-less dust inhaled
-less likely to spill Mountain Dew inside
-easier to open it up and mess with the insides
-you can see all the pretty blinken lights
Con:
-takes up valuable desk space
-at higher fan RPM, you may feel the vibration through the desk
UNDER the desk:
Pro:
-more free desk space
-quieter
-less distracting blinken lights
Con:
-more likely to spill Mountain Dew in it
-more hassle to mess with the innards
-more dust inhaled
-more likely to kick it
-can't see your pretty blinken lights
Temperature will not matter either way