When I put together Oubliette, I always end up drawing several versions of the page order out by hand. They look something like this:
However, now I've stumbled upon a useful site called corkboard.me which gives you a personal corkboard where you can organise post-it style notes. As soon as you visit the site it gives you a unique url for your board, and then you're free to begin adding notes. It's also great for to-do lists and other notes. I think it's perfect for planning layouts for short publications. Here's a screen grab of the one I just started for Oubliette Issue 6. Next, I just need to fill it up with the articles for the next issue.