SharePoint Enhancement Considerations when Using jQuery

Making changes to the HTML rendered by SharePoint comes with a few risks. SharePoint 2010 makes use of JavaScript to provide its own functionality, and you need to be careful whenever you are trying to customize that functionality. If you are working with HTML elements that you have not created yourself, you may not be fully aware of how and why they are used on the page, and your customizations could have an untoward effect. You will need to disable your custom JavaScript files before asking for Microsoft support.

If you find that you are making a lot of changes to the existing UI, that could be an indication that you are doing something wrong. Creating a custom master page and applying just the jQuery functionality required to that page is far more sensible than trying to contort the standard master page to fit your requirements. CSS can often be a better solutio if styling is all you are trying to do with jQuery.