There is surprisingly little research on this. Personally I find that contrast between different themes, that is when switching from say one website to another

There is surprisingly little research on this. Personally I find that contrast between different themes, that is when switching from say one website to another, is the most eye strain inducing. Going from reading black on white to white on black or vice versa just hurts. I keep everything black/dark on white themed since that's how most of the world works. I suspect many who use certain themes experience eye strain when viewing normal stuff and falsely assume it proves the efficacy of their theme.