Some mods need to load up in a certain load order. I suggest using the Nexus Mod Manager, it's very efficient. Because if you're lacking the certain DLC for a certain mod or another mod pack to enable THAT mod to work, you'll crash on start-up. Re-evaluate your mod list and check to see if you're missing any requirements.
For example, an armor mod that needs the Dragonborn or Dawnguard DLC to work. Make sure you check the requirement section of each mod, and make sure it doesn't have any extraneous requirements. What do you mean Nexus mods will not work? I've been playing several dozen Nexus mods with my Skyrim game.
