Among the most pressing functionality that comes to mind that hasn't been merged include:
VIA Kernel Mode-Setting - For those unfortunate souls still using VIA hardware, there is still no mainline DRM/KMS driver, even after it's been in development for years. There's still work ongoing, but nothing that was merged for the Linux 3.9 kernel.
Reiser4 - While Reiser4 is running fairly well after being in development for many years, the developers left working on this ReiserFS successor still don't see it going mainline anytime soon. At last check they were working on having a corporate backer or stakeholder to have a vested interest in the Linux file-system. Reiser4 patches for the Linux kernel are available but right now the most recent patches are for the Linux 3.7 series.
BFS - Con Kolivas' Brain Fuck Scheduler still isn't mainline but the developer simply hasn't been interested in pushing it. Fortunately, at least, he continues to make the BFS patch available for modern kernels, including Linux 3.8 as of last week. Some distributions are also shipping their kernels with the BFS scheduler.
Zswap - The patches for compressed SWAP caching still haven't been merged although they are still being worked on for hopeful integration in a future Linux kernel release.
Tux3 - The Tux3 file-system is still in development but hasn't yet been proposed for mainline. Recent Tux3 work includes an initial FSCK implementation and is said to be competitive with EXT4. Tux3 file-system development had stalled for a few years and was reignited in January so hopefully it will make it into a future Linux kernel release.
Reliable Nouveau Re-Clocking - Nouveau, the reverse-engineered NVIDIA graphics driver, still is in a poor performance position since it doesn't yet have full and proper support for reclocking the NVIDIA GPU for maximum performance. For most GPUs, the performance is stuck to whatever the frequencies were set at by the video BIOS at boot time. There is experimental re-clocking support for some GPUs, but nothing that's 100% reliable and would be up to the expectations of conventional desktop users/gamers.
Radeon UVD - There's nothing new on the AMD Radeon front for exposing the Unified Video Decoder under Linux with their open-source graphics driver. There's been Digital Rights Management concerns that have slowed down any open-source UVD work, plus AMD's open-source driver group is very poorly staffed in comparison to Intel and the proprietary driver groups.