I understand this would take some work to set up and maintain, but would be awesome if there was something like this:
A webpage you could goto, enter in the name of a Skyrim mod, and it would list other mods (that are currently in the database), that have conflicts with it (maybe just hard conflicts , such as CTD's, and as time progressed maybe list soft conflicts).
Sure something like this would take some work to get going initially, but users could submit a conflict with 2 mods as they arise, thereby expanding the database.
So ideally, you're getting ready to add a new mod to your lineup, you read the mod's readme, but some aren't so descriptive, I've seen that especially with Steam mods. Then you goto the Mod Conflict Database, enter in name of mod and see any known conflicts with other mods, that way by adding that mod you won't necessarily be limiting yourself to future mods, that you mightn't know about. For example, suppose you have Ebonvale mod in your lineup, but then find Touring Carriages, but then after reading the pages, you find out that there's a navmesh on the north road out of Ebonvale, that hangs up the Touring Carriage mod (I believe this is still a problem, might be fixed, haven't checked in a while). Another example I ran into, when I installed Uniques Uniques, I never knew it would cause an issue with Hunting in Skyrim mod, at that point I never knew about Hunting in Skyrim mod, but also don't think Hunting in Skyrim issue was mentioned in the Unique Uniques mod, had I known, I might not have gotten Unique Uniques.
Ideally, after it got going, mod authors could just list their mod on the database, with mods they know conflict it (of course they wouldn't know all mods, but maybe some). But after a mod is active for a while, with users adding info, it would give mod users a pretty accurate idea where they stand with adding a new mod, and wouldn't be limited to a users readme, or comments section on their mod page (heck, some mods have 100 pages of replies on nexus).