The answer to this question will depend upon what your site is about. If you have too many sections on your website then you will tend to use 3 column layout. The answer to this classic question is both layouts are good and work if you design your site well.
2 column layout:
1. Use when website has less sections. Use it with fixed width themes to give better appeal to users.
2. Generally if you have a 1028px or more width users tend to get lost when reading from left to right. So use two column with 770 px width.
MSN.com is a good example of high content , 2 column layout design.
3 column layout.
1. Keep one column fixed and dedicate it to navigation. Eg Left column on this website.
2. Use the right column to display Ads or some media material. This will make the center column shorter and readable.