Andrew, no, not really.
I am just thinking of ways to monetize plugins while still offering them as a free download to those who want to study and improve them.
One could provide a basic version hosted on WP.org and another full feature version to those who purchase an API key. Updates for the basic version would still go through WP.org, while I would control the full feature version.
Ideally I would imagine users making a donation right from their admin panel and receiving an API key upon PayPal confirmation.
p.s. I just realized that this works also for themes.