Hello all!
I found a really interesting thread on the Tyrant forums: http://www.kongregate.com/forums/65-tyrant/topics/187292-tyrant-battlesim?page=27
Contained therein are a couple of battlesim programs, that allow you to enter a mission, a commander, some cards, then run the simulated battle as many times as you wish.
They found that the best way to farm gold was to do Mission 90 with the following deck:
Atlas
9x Trident
1x Tiamat
It resulted in a win percentage of 99.72%.
Not every mission is in there, but if you're hard-up for gold, and can stand the monotony, then this is the way to go.
Good luck!
**edit: I tried this deck, and I've lost three out of thirteen fights...
***edit: I'm an idiot--this deck is for Corrupted Forces 4, I believe