In my opinion, these chem trails could be the result of the government experimenting with new engine designs that haven't been perfected yet. There are undoubtedly experimental engine designs to improve effency, reach higher speeds, etc, and these engines would produce strange "con-trails". Any chemicals released could be the product of incomplete combustion, or strange by-products of combustion.
The airforce is commisioning work on energetic ionic liquids. These liquids are entirely composed of ions at or near room temperature. No solvent (water or organic) is present in these liquids. One benefit of these liquids is that they have neglidgable vapor pressures, which means that they don't evaporate and therefore are much less hazordous to work with. The risk of fire or explosion in the event of a leak is greatly reduced. High energetic ionic liquids could be used as fuels and/or explosives, and would be much safer to handle. Think of being able to fuel a plane with a liquid fuel that wouldn't evaporate. While some chemical protection would still be needed, you wouldn't need any kind of respirator.
Now, as far as I know, these types of fuels are still in the theoretical stages. However, if the military is looking into these types of fuels, what other fuel and engine designs are they looking at. Personally, I'm not worried. I don't think it is a government conspiracy of any sort. However, such work isn't public knowledge in the interests of national security. Think of the situation from the government's standpoint. They can fly these aircraft around for testing purposes, and their con-trails may be strange looking. However, no one could reverse engineer an engine design from a con-trail, so who cares if people see these things?
Ryan