It can never hurt to apply. I know there is an application fee, but GRE is just one of many areas schools weigh for applicants. I was just accepted (1 or 2 students) into a PhD program at a very good school and my GRE percentiles (specifically quant) are not great: 37th for quant and 63rd for verbal. I took it twice (after 3-4 months of studying) and figured I'd hit a threshold. If you have other components of your application that will make you a good candidate, then GRE alone shouldn't hold you back. Write an outstanding personal statement.