I think I've discussed how to format your manuscript before on the blog, but more issues seem to be coming up with both my own clients and in submissions of partial and full manuscripts, so I thought I'd make some additional suggestions.
First, use Microsoft Word if possible. This is the program that most agents and editors prefer for both submissions and editing, and so you need to be on the same page as everyone in the industry. WordPerfect is ok, but sometimes mistakes can happen in the conversion to Word.
Do not send agents a PDF if you want them to provide edit suggestions, and certainly once you're a client you'll need to send agents things in Word. Also, the Kindle can't read PDF files.
If you use Microsoft Word 2007, make sure that you're using the "Word 2003" style and saving it as a "Word 97-2003 document." Why? Because many agents and editors don't have the new version of Word yet and haven't downloaded the software needed to convert Word 2007 files for use on an older format.
Learn how to use track changes for Microsoft Word. This is an amazing feature that allows agents and editors to make editorial suggestions directly into the manuscript.
Make sure to include page numbers and either footers or headers with your name and/or title. Some agents and editors still print partial and full manuscripts for reading. Friday afternoon they'll print up a bunch of submissions, stuff them in their grossly overweight messenger bag, and lug them home for weekend reading. If you don't include page numbers and headers/footers and the agent isn't extremely careful, your project pages will likely get scattered about.