No, I don't mean "Show Invisibles," and the "Default Line Breaks" setting doesn't seem to affect anything. The problem is that TextWrangler is displaying files as if linebreaks (\n) don't actually break the line. For instance, if I turn softwrapping off, the entire document ends up on one ridiculously long line. It does, however, properly display carriage returns (\r) as one would expect.
I'll try out Smultron. Thanks for the tip.
Edit: I tried out Smultron, and it certainly does handle both \n and \r properly. That's good. The bad news is that its command line tool isn't good enough, and I hate how it forces you into an MDI thing and quits when you close its window.