When your plugin is hosted on WordPress.org, this isn’t a problem at all. But if you’re selling your own work, or hosting it on a non WPORG resource, there are other concerns. You see, if you host a plugin on WordPress.org, your plugin can’t have it’s own updater script. You have to use the default .org updater. This is just fine, except when you have an add on that you want to be pay-only. Then what?
Take a look at Easy Digital Downloads. You can get the main plugin from WordPress.org, and if you buy add ons from their site, they get magical updates too! How did they do that? They put an updater script in the main plugin which is then called by the paid extensions. You can even use their Software Licensing add ons to run your own updates on your server! If you want to sell on their site, they’ll help you take care of that too.
Todd Lahman also has an WooCommerce API manager, so if you’re using WooThemes, you’ve got that covered too.
Speaking of self hosting, if you’re hosting your own code on Github, then you want to use Andy’s Github Updater. While it’s not allowed on .org (sorry Andy), this will let you push updates from your GitHub or Bitbucket hosted WordPress plugins and themes.
My buddy Norcross has his own free updater for you as well.
Jeremy Clarke has a automatic theme/plugin updater as well if you still want to be self hosted.
If you’re using ThemeForest, there’s the Envato WordPress Toolkit, which your users (not you) will need to install on their sites to get updates. I don’t know if there’s a way to include an updater in your packaged theme or plugin, but that toolkit needs to be all over the place for users. That it’s not brings all the issues you see with their products being out of date.
There are hundreds of other ways around this. And really, there’s no excuse to not keep your plugins and themes up to date, no matter where they live. Keep those users updated and make it easy for them to do it! What resources do you use when self-hosting a plugin or theme, to keep it on the up and up, and keep everyone updates?