Some of the big problems are wifi, bluetooth, sound and video related. Most of these problems are a result of proprietary drivers/hardware. I have problems with bluetooth that my keyboard won't connect after a reboot. Configuring the spdif raw output is a pain(eventually got it running properly with a custom .asound configuration). Cheaper sound cards only support one channel, thus causing one application to block another (there are workarounds, but even for the tech-savvy this is a pain). Video support, you are at the mercy of the hardware.
For me, Linux is ready for the desktop, it's just that some hardware's not ready for Linux.