I am using the Nexus Mod manager. I have got a problem with quite frequent ctd. It just shuts down the game, no errors. I was thinking of maybe trying to disable mods in the Nexus Manager but can it screw things up even more to enable and disable mods in this way?

Also is there some list on how the load order should be?

No. Don't disable mods mid save and then continue to use that save.

Well, strictly speaking if the mod contains no ESP/ESM file (like a texture mod), then you can get away with it. But anything with a plugin file is risky, and anything with scripts is definitely a huge no-no.

For load order, you'll want to use http://code.google.com/p/better-oblivion-sorting-software/.

BOSS for your load ordering needs.

TES5Edit for your cleaning up ESM's and ESP's. (Decrease chance of a CTD by removing a lot of "dirty" edits or duplicated entries and what have you). (Atleast that's my understanding of the tool, probably not close to the real truth, but there abouts).

Also, in a spoiler tag, post your current load order, I'll take a look and see if I see anything out of place, as will most people on this forum.

Edit: ninja'd for the BOSS thing, and he has a link too..