Hole punching as it pertains to file-systems is marking a portion of a file as being no longer needed and can then be reclaimed. With Linux 3.9, there's hole punching support for non-extent-mapped files. Hole punching support has also come to other Linux file-systems.
The EXT4 updates in Linux 3.9 also address some race conditions, take care of some potential null pointer dereferences, memory leaks, and an optimization in the JDB2 layer. There's also some enhancements to the extent status tree.
More details on the EXT4 file-system updates can be found with the Ted Ts'o pull request.