[This answer][1] is really brutal on the eyes however I think it's key to have filenames and commands with that kind of formatting.

Maybe perhaps toning it down a bit? Similar in shade to the blockquote perhaps? Example:

`ouchy ouch commands hurt eyes`

> softer nicey nicey commands not so much.


  [1]: http://askubuntu.com/questions/13077/is-profile-sourced-by-bash/13182#13182