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In years past, in the studios that I've worked in, they often used an Eventide Harmonizer (or other similar product, eg, the h8000) to do MIDI controlled time compression / expansion (without pitch shifting) of the audio tracks so that the cues / hits line up perfectly.  If they didn't need the cues to be absolutely perfect, I've seen guys just route the MIDI from one of the control wheels on a synth to the MIDI input of the Eventide and line up the cues amazingly well just by ear.

These days, there are software plugins available for almost every common audio recording / editing program that will do the same, and some will even automate the process of synchronization.  One can even get one's feet wet in synchronization using something as simple as Windows Movie Maker:

http://www.wikihow.com/Synchronize-Video-and-Music-With-Windows-Movie-Maker

Compared to splicing in or out segments or even loops (where this is musically acceptable), as long as the required degree of time shifting is not excessive, the changes in tempo with the Harmonizer method won't be noticed, and it's usually a much faster way to work.  An intermediate approach is to splice in / out segments to get close, and then do the fine tempo adjustments with the harmonizer or with equivalent software.

Tom M