I researched and wrote this long treatise. Lucky for all of you, I did a preview and in the process lost it. I'll simply my long windedness.
The FAA says all design speed will be in EAS equivalent airspeed. In a perfect world, EAS=TAS=CAS=IAS at seal level on a standard day. EAS is TAS adjusted for density. At low altitudes (under 10k) and low speeds (200kts), EAS is close enough to IAS for practical work.
From what I can tell, Vne can be derived either from structural limitations which are usually defined in design dive speed and from flutter limitations. The Vd is accurate based on IAS.
Flutter is a vibration, often of a control surface but sometimes of a wing http://www.youtube.com/watch?v=kQI3AWpTWhM
that is not dependent on how many air molecules hit the surface but on their speed, thus while the discussions I saw spoke of it in terms of IAS and TAS, one can see why TAS seems a natural response.
My suggestions that Vne was a TAS function was based on my readings about flutter and my experience flying jets where our IAS also had a TAS readout and where we had varying red lines that changed with altitude. I was part right but not all right. Paul's observation that Vne seems usually associated with IAS is in line with most light plane experiences we have.
In the event, Paul and I both agree that the POH for the specific plane is the source we should abide by. Paul is right that in most cases the reference will be in IAS. I hope this clarifies any confusion I may have generated. I have to admit, researching this topic is pretty obtuse.