I'm using synergy to share keyboard/mouse between OSX and Win7.
Unfortunately for the mac, the commandkey seems to be bound to the alt key. How do I move it back to the command key? Or the ctrl key?
Change the assignment in the Synergy configuration:
If you don't know how to configure synergy via configuration files and use a Mac as host system, download and install SynergyKM, which provides a GUI-based configuration to Synergy.
Open System Preferences » SynergyKM, select Share my keyboard and mouse, and in the Server Configuration, add a screen for your Windows system and open Screen Options. Change your modifier key configuration there.
I don't see where you specified which machine is your host.
If you are using the Win7 machine as host, then the following configuration is what I use to make the keys work properly on the Mac client if you are using the text configuration: