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I've been using Perian without the preference pane since I wrote this post (actually slightly longer!), and have noticed no problems at all.
You can use a restricted version of markdown formatting here. You can use the toolbar above the text field to make this more painless. For more information about markdown please refer to the markdown cheatsheet.
The preference pane was annoying to me as well so I followed these instructions on my system yesterday. Have you had any negative effects from doing this? Great tip!