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if you were building something, say a coil gun, would it be best to use a bank of higher voltage (300+V), lower uf (80-120uf), or a few capacitors of say, 1000uf 50V or lower?
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Well, power (measured in columbs) is still power.  Here's the equation you are looking for
capacitance * voltage= power

Put your numbers in and whichever combination yields the larges power, is the one you should use.  Here are your numbers->

120uf * 300v = 36,000
or
1000uf *50v = 50,000

As you can see, the lower voltage setup will be better.  Typically, a 50v 1000uf capacitor will be significantly smaller than a 300v 1000uf capacitor.  Also keep in mind if you did go the higher voltage route, you are going to have a hard time safely making 300v.  Much easier to stick with the lower voltage anyway.  Remember anything over 30V can SHOCK you and capacitors arc and can KILL, so no touching.

does that mean, the higher the uf the greater the oomph? I am researching parts for a joule thief to be used in a circuit that if done correctly will continuously recharge the battery being used and provide enough power to run a small dc motor.

i want to make an E-Bike that does not need recharging.

how much is a simple neon pulse generator? I'm having difficulties finding one via Google.

It has to be balanced with your actual coil but in general more voltage and middling capacitance produce the best results.