Input formats can be a challenge for folks who are new to Drupal -- especially if you've bowed to the pressure to use a WYSYWYG editor on your web site. Luckily, the input format system has some good options to help control things.
One think you'll need to think about is which users will be using your site, and what sort of tools are they going to need. Are they savvy enough users to be able to use some more crunchy formats, like Markdown? That's a possibility, but it's probably not the case for most of you.