Today I needed to add the newest version of jQuery (1.7) to a custom Drupal 7 theme that I was building. I initially used the jQuery Update module and hacked the replaced version of jQuery with the version I needed. I know, this was not the best practice, but this was a rush job and I was in a hurry (don't hack the core, or any contributed modules for that matter!). Everything was working fine until I wanted to add a new field to a content type and the form quit working in the admin overlay, which was using the Seven theme. Crap!
The Right Way
Now the new version of jQuery loads for my theme only and won't break any other themes.