Plugins are various extensions to the basic functionality of WordPress software. When added to WordPress, they provide new features without changing, or breaking, how WordPress basically works. WordPress is the house, the fireplace is the plugin. To digress. In real terms, a fireplace is a pretty damn big plugin. It’s probably not the best example to use. But since blogging is as much a virtual world as real, and we’ve all seen the Matrix so we know what virtual means, we won’t sweat the details on building that fireplace.
.com does not allow plugins. .org allows plugins
Now the above is not totally true. The .com version has plugins, but only the plugins that Automattic (Automattic is the company that runs WordPress.com for you) thinks you’ll need or is willing to allow you to run. If .com comes standard with a brick fireplace plugin, you cannot change it to a stone fireplace plugin. The .org version allows you to add any plugin available, possibly even that stone fireplace. In the most extreme case, you could create your own plugin. Creation is not to be taken lightly.
Most of the differences listed below may simply be due to plugins that are automatically installed when you use the .com version. That’s a hypothesis at this point, not a researched fact. When you use the .org version, you’ll have to hunt down and install any of the plugins that might be missing below. You may question, why doesn’t WordPress.org distribute the same plugins with the .org version as is installed when running your blog on .com? That’s a mystery along with the list of the plugins that the .com version seems to use automatically.