While I mostly use CNX2 to process my NEF files, I've recently incorporated Lightroom into my workflow. I've found that Lightroom does a great job organizing my photo collection, while I still prefer CNX2 for post-processing - mainly due to its more reliable decoding of NEF files.
However, this was made a little cumbersome by Adobe's less-than-wonderful "Edit In" feature. External editing of Raw files in Lightroom is only possible in Photoshop... Other editors will just get a TIF version of the same file.
Photography Life wrote some nice explanation for why Adobe decided to prevent us from editing Raw files in an external software. But... what if you really don't care about that limitation - and you still want to open the NEF file in an external editor??
My workflow was getting a little difficult to use, so I've decided to take some action and make my own solution.
I've prepared a small script, that instead of opening the TIFF (as Lightroom intended) - passes the NEF filename to CNX2. It doesn't depend on CNX2 location on your HD - you just need to define CNX2 as the default program to open NEF files in Windows.
You can download and use it, free of course. Just read the release notes to check the necessary configuration, and of course, as with any freeware, use it at your own risk.
Link to NEF launcher (Rapidshare link).
Let me know how it worked out for you.