I think there are probably dozens. I'm always kind of amazed that people put up with Chemdraw, but I guess it's pretty entrenched. Here are the first three alternatives that popped out of the repositories for me.
BKChem: This is what I use. Simple, written in Python.
XDrawChem: This one's been around forever, but hasn't been updated in a while.
ChemTool: Haven't used it, but looks like it's getting updated more than XDrawChem.
I use BKChem, but it can be a little finicky. XDrawChem is another open source one that's pretty commonly used. Lastly, Wikipedia has a list of a ton of them too, both free and non-free.