The best way for a pilot to avoid a thunderstorm is to simply not fly when there is a good chance of one occurring. However, when the weather report inevitably reads scattered thunderstorms or a chance of thunderstorms throughout the summer season in many locations, not flying is not really be a practical 
Hence, Patrick Flannigan has made an excellent blog post about thunderstorm avoidance on AviationChatter.com. In it, he explains the tell tale signs of a thunderstorm approaching and what parts of one to completely avoid. Patrick also explains that staying down low and avoiding the rain shafts, a preferred method of VFR pilots, has its drawbacks. In fact, he suggests a better way might be to get on top of the weather and weave your way through the buildups.
At the end of the post though, Patrick clearly states that there is no shame in choosing not to fly or in landing to wait out the storm as that might be the safest and smartest course of action. The blog post is well worth reading – especially with the summer flying season upon us.