One of the main things I wanted to know about the Sony a6000 was could I use my Nikon SB 900 & Nikon SB 800 Flashes with my Nikon Pocket Wizards. The answer is Yes! I actually think the pocket wizards work better on the Sony than on my Nikon D700. I had zero mis-fires, where as on my D700, I was always fiddling with the pocket wizards to work properly and even trigger. To get the pocket wizards to work on the Sony a6000 I had to go into the software and make them basic triggers, this means you have to work with your flashes manually no TTL. I also chose a channel for all of them (trigger and receiver) to share. So here is a list of the Pocket Wizard transmitters and receivers I got to work on the Sony a6000:
The only difference between the Nikon D700 & a6000 is sync speed, I can only get 1/160th max sync on the Sony a6000 with no TTL, but it's not that difficult to work the flashes manually.
Hopefully this will help others with this decision because it concerned me for the longest time and was the only decision not to buy the Sony a6000 because I have so much invested in my Nikon. Side note: the files seem to be way sharper than my D700 I almost don't need to sharpen them in post. The photo below was shot on standard profile