I upgraded to macOS Sierra today on my work laptop. I hit a few minor niggles related to some keyboard hacks I had in place. The first was working around the fact that Karabiner no longer works in Sierra, which is well documented by Brett Terpstra here. I don't rely too much on the "Hyper" key, so actually the main thing I cared about was remapping Caps Lock to Escape. This, by the way, has been a game-changer.
I uninstalled Karabiner and Seil, which I had previously installed to accomplish my hacks (although I was never clear what Seil was for).
The second issue was related. I type on a Das Keyboard Model S Ultimate. Before the upgrade, I swapped the option and command keys because it is natively a PC keyboard. This stopped working in Sierra. Despite setting the modifier keys to be swapped, the behavior did not change. So, I used Karabiner-Elements to accomplish the swap: