This weekend I gave feedback to a friend on his novel submission packet. While I don't believe submissions must follow a rigid set of manuscript rules or always risk instant rejection, authors should generally stick to the basic formatting guidelines so editors can focus on what really matters--your story--instead of that crazy font you printed your story in.
For my money, the best online resource for proper manuscript guidelines comes from William Shunn. He presents the formatting guidelines in an extremely visual way as actual short story, poetry, or novel submissions. New writers would to well to study up on these examples.