Dark energy. Branes. Multiple dimensions curled up so small we can't see them. Difficulties unifying quantum mechanics with general relativity.
I wonder if we're due for a paradigm shift. The current environment, at least from an outsider's perspective, looks a lot like we're piling epicycles on top of epicycles, or positing the existence of luminiferous aether: we're extending our theories in multiple directions through the use of phenomena to which we're "almost totally blind" (to quote Sciam's Dark Energy article).
Maybe we're due for another Copernicus, Newton, or Einstein to fundamentally reexplain the world around us.