Gems: The cheapest and easiest way is to farm level 5 NPC with your ballista waves. If you don't care about the resources and just care about gems, you can send the ballista waves at NPCs every 15 minutes and still get gems from them sometimes.
Medals are a little different:
Cross/Rose/Lion: Farm these in level 1-3 Valleys.
To farm a valley, send attacks to land every 10 seconds or so. Once it hits (and captures) the valley, quickly abandon it before the next attack hits so that it re-spawns. Do this until you are bored or until you have the desired amount of medals.
Honor: Farm these in level 4 NPCs mostly with my ballista waves.
Courage/Wisdom/Freedom: Farm these in level 5 NPCs with ballista waves
Justice/Nation: These are the hardest and most expensive to get. The easiest way I found was to attack a level 10 NPC with a normal Hero Leveling wave, and then follow that 100k warriors that will and every 4 minutes afterwards. Any less than 4 minutes and you lower the drop rate, and more than 4 minutes and you increase losses that you will suffer.