Here is a list of some of the ‘must-have’ tools to help you troubleshoot issues with mods.
Oblivion Mod Manager (OBMM) v1.0.3
Organize load orders, update BSA files to register new textures and meshes, detect conflicts between mods, create and use omod files.
The ‘swiss army knife’ for Oblivion mods. Everything you need to detect issues, change load order, repair save games, merge mods or create patches.
Oblivion Mod Removal (OBMR) v2.01
Automatically remove all files related to a mod.
Note: watch out for files shared by several mods. You may have to reinstall something after cleaning up a mod with this tool.
Nice little utility specialized in analyzing conflicts between mods. You can select which mod you want to analyze and which type of record you want to include in your report. Perfect tool to go deep into the details of overlaps and conflicts between mods.