HeyThis is for way up north. But there are some mixed-sex onsens where you must wear a towel over your bits.
I think it spoils the point but I guess it depends on the onsen. And also, don't worry about coming into close contact with a guy because although there are mixed onsens, they are sometimes segregated by an imaginery line.
But these places are rare all thanks to the government who imposed extra taxes on the onsens for keeping this traditional mixed bathing option. So, most of the onsens converted to single sex. As was their plan.
You can still find them up north. I know that their are some in Miyagi and Fukushima. But a long way for a bath. But worth it if your in the area.
I use this website for onsen research. It lets you know everything from water pH to cost. It even lists if a swim suit is allowed.
http://www.secret-japan.com/onsen/
Then click on the "Search" link at the top of the screen.
Hope this helps
Adam