It's all about marketing. With an application certification you can play-up the certification in your sales materials, which would be an important difference if competing software was not certified. On the flip side, if other competing software are certified and yours is not, if MAY suggest that your software is inferior somehow.
It is really going to depend on what field your software serves, whether you're willing to make the financial investment for the certification process and whether you think that certification will boost sales enough to justify that investment.
If you decide to certify your app, I would strongly suggest that you develop a marketing plan on how you're going to use that certification. It would be a shame to spend the time and money to achieve the certification and then not take advantage of it.