Board Thread:Oblivion/@comment-92.33.163.139-20130307235228/@comment-5469467-20130310065519

Depends. If you're playing Oblivion, doing certain quests (including those for the Dark Brotherhood) and actions will lower your reputation. That said, doing other quests to raise it will theoretically balance it out.

In Skyrim, as Blades59 mentioned, it doesn't really damage your repuation (aside from getting caught commiting a murder or something).