In all seriousness, modding Skyrim is a delicate balancing act, even with a small number of mods. When you get into triple digits (or even mid to high double digits) it gets even harder. Its not helped by the fact that it is not possible to truly "clean" a mod after removing a mod. Even if we manage to isolate the mods that are causing you issues, it would still be best for you to start over.
Even if you are not hitting the RAM limit, there is a good chance that running a lot of heavily scripted mods then you may be overloading the papyrus engine.
It would really help if you could post up your most recent BOSS log and papyrus logs. That would give us more to work with while trying to help you.
Whatever you decide to do I would say that you have to be aware that getting all your mods to work together will take a lot of time. That is just unavoidable with that many mods.
Personally I would do the following:
1) reinstall Skyrim (making sure you have a backup of all the installers for your mods and that you completely clear out your skyrim data folder) and whichever DLC you have.
2) Install the latest version of SKSE.
3) Install the latest version of Wrye Bash.
4) Download the latest versions of any of your mods that need updating.
5) Download the latest versions of the Unofficial Patches.
5) Install your mods one by one using Wrye Bash. Make sure to install your mods in the correct order (I'd advise following the STEP guide for an example of what order to install different types of mods in), and check for any conflicting files (particularly scripts).
6) After installing 5 or so mods, use BOSS to sort your load order, clean any dirty mods, and load your save. Repeat until issues arise, and then open up those mods in TES5Edit and examine the conflicting records.
Even if you do this, and locate the major causes of your problems, my advice would be to abandon your save and go back to a save before you installed any mods.
Edited by Azakiel, 17 December 2013 - 10:45 PM.