This is a great piece by Sam Ro of Yahoo. It points out clearly the biases that occur with non-GAAP earnings. I would consider it an important educational piece for those not versed in the "game of earnings".
With non-GAAP earnings always being higher than GAAP earnings, it shows the story that management often wants to "paint" for you. Are items excluded when it isn't to their advantage and included when it is? Being higher all the time, makes you think.
Historically, adjusted earnings were the purely the work of the Securities Analyst. It seems now days that management is working hard to frame their financial position to their best advantage. Now there is a significant degree of management discretion even in GAAP earnings. The non-GAAP earnings are items that the accounting rules specifically exclude from GAAP.
The positive thing about companies providing both GAAP and non-GAAP earnings is that there is usually a reconciliation between the two. You can throw out those "adjustments" that you find inappropriate. The challenge is that some of the items in the reconciliation are hard to clearly pin-point.
You make the call, but be aware of potential biases.
