I am a pilot, and understand navigation systems, which was why I said the bad guys would want to jam GPS, VOR, NDBs, ILS/MLS, as well as old fashioned COM frequencies. This would leave only dead reckoning... Given pilotage is worthless is actual IMC.
One could also place the jammers in crowded areas, making them impossible to target with missiles without a lot of collateral damage.
All that being said this is much more likely a good plot for the next (or a previous) Die Hard movie than a real hard core terrorist plan. But simply frightening the flying public for a mere 5 minutes would be enough to cause millions in economic losses for the already hurting airlines.
Are there ways to handle this? Yes, old school "strips," and greater separation manually... But what if the controllers can't find the real targets? In VFR conditions everyone must see and avoid anyway, and IFR flights would probably have to revert to VFR if in VMC. But what of a bunch of IFR flights in actual IMC? TCAS you say? What if said bad guy could spoof TCAS as well? TCAS would likely handle the huge amount of targets even worse than the TRACON software (might even crash... in the software sense). Add a power stuck mic to jam up all the COMM frequencies and you cause a lot of trouble indeed. Pilots must follow a discreet set up rules in this case, but they are not perfect in that they cannot help a jetliner that has had a headwind the whole way, and is low on fuel with now opportunities to make it to a VMC field.
I'm just saying I believe with enough resources it could be done. Create a ton of fake targets near a busy airport in bad weather. Jam all COM frequencies. Jam GPS, Jam the ILS/MLS. Jam the VOR signals, and any remaining NDBs. It may not lead to loss of life if the bad weather was not too far widespread (such that IFR flights could proceed to VMC and land VFR), but either way it would cause a lot of monetary damage, and a lot of terror in the flying public...
Encryption would be a very good thing for ADS-B. As we update the system from old school mode C, we might as well be countering these things.
Just put your name down on the list of travelers who get the full Monty of invasive security theatre, er... screening... I hear the TSA has hired a new batch of proctologists just for the petition signers...
Seriously, I would be a little concerned. Since they create those no-fly lists, etc. from all over the place, even the internet...
For large values of one, one equals two, for small values of two.