Recently, the Guide to Literary Agents blog wrote an excellent post about properly formatting queries.
I do recommend you check it out. However, I have a couple quick notes to add, for those of you wanting a bit of a quicker and more repeatable method. Pasting into notepad is certainly a sure-fire way of removing formatting. However, it isn't the only way. Here are some other ways to remove formatting.
If you use Google Chrome as your web browser, there is a built-in "paste without formatting" command. Normally, the keystroke for pasting is CTRL + V. However, if instead you type CTRL + SHIFT + V, then it will paste without formatting. This makes typing your emails quick and easy, and you'll strip out the formatting no problem.
If you use Google Gmail, then you have another easy way to remove formatting from an email. In the toolbar where the Bold, Italic, etc., tools are, there's also a Tx button. The Tx button removes formatting from selected text. So, you can paste your text into your email editor and press the Tx button, which should remove any weird size, font, etc., changes.
If you do use Word to write your queries (checking for grammar errors, etc.), then there is a way to at least remove unwanted formatting changes. When you paste in text, instead of using standard paste, go to Edit->Paste Special and select Unformatted Text. This will let you paste in text and use formatting of wherever you're pasting to, rather than where you're pasting from. Your text will still have formatting, but it will be consistent formatting throughout, which is the important thing. (Note that if you do this often, you can create a Macro in Word than you can then apply to a keystroke, say the above-mentioned CTRL + SHIFT + V. Go here to find out how to do it.)