Zero-padding in STFT
For linear time invariant filtering, the best methods are overlap add (e.g. http://en.wikipedia.org/wiki/Overlap%E2%80%93add_method) or overlap save. If latency is an issue that can be improved with "block convolvers" or "segmented overlap add" (e.g. http://www.cs.ust.hk/mjg_lib/bibs/DPSu/DPSu.Files/Ga95.PDF) 

If the processing is time variant, things get a lot more complicated and the right choice of FFT length, analysis window, step size &amp; synthesis window really depends on the specific of the application.

If you don't want to do any processing but just data analysis, the only thing that zero padding does is interpolation in the frequency domain. You get graphs with higher resolution but not more information.