Hello. ENB and stereo 3D vision are compatible!
All you got to do is to ensure you follow this points for proper installation:
Drop ENB DLL in Skyrim root folder
Rename ENB DLL to something like d3d9ENB.dll (to make it load second as proxy)
Drop the Helix d3d9.dll file in your Skyrim root folder(so it will load first)
Edit your DX9settings.ini to load your ENB DLL as proxy, i.e :
[General]
UseEndScene=false
ProxyLib=Z:\Steam\SteamApps\common\skyrim\d3d9ENB.dll
________/\--------/\-----------/\---------/\---------/\------------/\
!! modify this path according to where YOUR Skyrim install folder is !!
I'm using this stereo/ENB configuration since 2 years now and it is working pretty well. Only ENB bloom looks weird but you can easliy desactivate it and then rebalance you lightings with skyrim bloom instead (vanilla bloom is stereo-friendly). If you've got disturbing stereo shadows on rocks or grass/ground you can edit bdeferredShadows=0 in your SkyrimPrefs.ini (at a cost that some ENB features will not work, and you will not have shadows on grass, but it is still worth it!) Once you've properly set, you will experienced ENB Skyrim in stereo, and then you will not go back to 2D world, believe me!
Cheers!