Well the key to an airliner (or any other vehicle) surviving a real EMP would be having engines and flight control systems that don't require any kind of computer assistance. Hydraulic control systems powered directly by the engine and not relying on a computer to operate the valves would continue to function, as would cable-driven control systems. Simple electric motors may also continue to operate (larger motors tend to be EMP-resistant, in smaller motors there's a chance the EMP could burn out the windings or arc over and destroy the brushes) which means we can assume you'd still be able to pump fuel into the engines of most jet airliners.
Thinking along those lines I imagine the remaining DC-3 fleet would be almost entirely unfazed by an EMP (save for any retrofitted avionics, radios, etc. which would likely be fried). Similarly the Boeing 707 would probably not have a problem, nor would early-generation DC-9s, 727s, and 747s - you would lose any retrofitted flight management computers, but they are generally not essential to operation in the earlier-generation aircraft.
There are probably several other models still in service (or hanging around various boneyards) which are at least somewhat EMP-resistent.
If we assume a Revolution-style apocalypse where absolutely nothing using electricity works you're rather worse off: only aircraft which have cable-driven controls (or hydraulic backups with manual valve actuation & direct pressurization from the ram air turbine) would have functional flight controls. Thats a much smaller subset of the fleet these days, but the planes do exist - as Terry pointed out the 727 and 747 both have non-electric control systems available.
If we assume magnetos can still generate a spark the DC-3 other planes of its generation would be the clear winner: The engines would continue to run until stopped (the engine-driven fuel pumps would continue to feed the engine fuel). Aircraft like this could even possibly be restarted (using shotgun starters or pull starters, and a little help getting fuel to the engine until the mechanical fuel pump could take up the job).
If we assume magnetos would also stop working then at least you'd have flight controls and the ability to make a controlled emergency landing somewhere as you could in the other planes mentioned.