Of course look up Sheldon's section on frame alignment.

I have used the string method to check my rear triangle. I also ran string to check my front fork for simmitry. I have used large C Clamps to check my dropouts and derailleur hanger. And I have held a straight edge to the tubes to check for bending. I have also pinged a stripped down frame for changes in sound along the tubes and welds. Really these simple tests just give ya piece of mind.

Twice I have had to trash a frame. One had two tubes bent and the other pinged out soft rust spots on the inside of the the seat and top tube. But I knew these bike were shot before even checking them...