I get a black screen freeze every now and then, turned out that was due to a known problem with current drivers for the 7970 and possibly entire 7000 series even if 12.6 was supposed to have solved it (I'm on some 12.8 beta I guess it is.) so yeah troubleshooting can be quite difficult, mod conflicts for example would probably be minimized by proper load order but if two plugins modify the same thing then one of them will of course override the other depending on load order, usually it's minor and doesn't cause stability problems but if scripts are involved or other more sensitive data then that changes things a bit.
EDIT:
One thing I truly worry about is that older mods having older esp's might not work well with newer Skyrim versions. Like suddenly I just want to disable all mods that aren't meant for 1.7, for example.
{edit} Skyrim crashes immediately during loading without the INI files.
Patch 1.6 changed (fixed) a Navmesh (AI navigation / pathfinding data, I can't describe it very well.) related problem (finally) and that required the affected mods to be re-saved by the 1.6 based Creation Kit (With patch 1.7 only the exe was altered so I don't think we'll get a update to the editor yet, would be nice for some features currently used but unavailable for editing - for example in Dawnguard.) anyway back to this without those updates the affected mods can be unstable.
Patch also changed some script behavior which required changes to several mods and utilities like SKSE, I got a crash from a mannequin fix due to this because I failed to notice it had been updated - http://skyrim.nexusmods.com/mods/10652 - so there's probably a few mods affected by this as well.
Even worse would probably be the older mods made via third party utilities, TESVSnip was found out to cause certain edits lead to record corruption which resulted in various glitches in the actual game.
These are just some suggestions, there's many other things to consider like just what you mentioned about drivers being up to date and working correctly or VRAM usage when using several texture mods, bad models (.nif) files can also be unstable such as seen with early releases of some of the parallax enabling mods.

That thing about Skyrim crashing without a ini file is weird though, rename Skyrim.ini and SkyrimPrefs.ini and run the launcher, it should use the game folder skyrim_default.ini as a preset and yield a new Skyrim and SkyrimPrefs.ini file correctly but maybe you've altered uGridsToLoad from the default of 5 to say 7 or 9 instead?
(Those edits store in the save game and crashes the game if you try to load that data without some edits first via SaveIni and Set commands - and something else I've forgotten - to reset the value back to five.)
EDIT: I'm not expert or anything like that though, these are just general suggestions at best, might help somewhat at least, there's probably a lot of stuff I've missed to mention though and a lot of other possible reasons why you're getting these issues.
