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I hear both good and bad things about Netbox. It's got an API and you can plan everything up to and including which cables go from which ports to which and what category they are.

"Excel is the third-best tool for any job in computing. Second-best is prohibitively expensive. The best won't run on anything newer than NT4... and the sole developer died in 1998."

I use Visio for planning because I like downloading the custom stencils and stuff so it looks pretty, but generally use NetBox for long term documentation.