I'm also new to DomiNations, but here's an Iron Age farming base I just designed and it seems pretty decent for just getting started. I've been playing games like this for quite a while now and put some of the things I know from them into this design. I also used some of the suggestions mentioned earlier in this thread. Thanks Guys!
Some of the features:
1. Uses the Acropolis, which reaches both Garrisons.
2. Centralized Catapult, inside it's own compartment, with a range beyond both markets and both mills.
3. The Garrisons are also centralized, covering pretty much the entire base. The gate locations also give them easy access to all sides of the walled-in area.
4. All but 4 buildings are in contact with roads. You can make it all but 3 if you move the mercenary camp next to the temple. I may actually do this myself.
What do you guys think? See anything you would move around? I look forward to hearing any ideas or suggestions that might improve the layout. Thanks!
UPDATE:
Decided to leave the mercenary camp where it is for extra protection on the top side, and put traps near the bottom towers instead. I think that should be a fairly even tradeoff.