As great as Mods are you should just look into SpoutCraft, Spout has support-API for a lot of major addons like;
- New ores
- New armors
- New mobs
- New terrain
- New items
You can force your users to download the spout client to play on your spout server so you know they are receiving the same benefits, or you don't have to and they can just sit around without half of the awesome content you installed on the server, Your Choice!
I know this doesn't help you with your 'Mod' support but let me say modding is a headache and im sure you will find something equally as awesome in the spout community.