Generally, you want to target pitchers with good Strikeout (K) rates, and Whips as close to 1.00 as possible. A low whip indicates a pitcher has the ability to keep batters off the basepaths, and pitchers that can get Ks are generally more capable of getting out of any trouble they may get into. A good strikeout to walk ratio (called K\BB) is an indicator of a pitcher with good control of the strikezone. In general, good pitchers will have a K:BB ratio of at least 2.25 - 3+ strikeouts per walk. (Higher the better)
If you focus on these metrics instead of Wins/Losses and ERA, it can help you identify quality pitchers, which is what you want in fantasy baseball. It can also help you identify pitchers likely to improve, for example, a pitcher with a 4.50 era may have a low whip (1.15) and a good strikeout to walk rate (ie 3:1) indicating that he may have just had a run of bad luck, and could be primed to improve upon his overall numbers.
This isn't an exact science, but if you can understand what the peripheral stats mean, you'll be better equipped to evaluate the pitchers you'll run across during the course of a year.
Now if you have a pitcher with a solid track record, decent to good peripheral numbers, and that pitcher plays on a team with a good bullpen and a high powered offense (think the Mets, etc) you may bump their value up a bit, since they are likely to end up with more wins in the long run.
Hope this helps,