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In the free version you must know the native installer switches and pass them through with install args. In the paid versions you have a ubiquitous install directory option where Chocolatey determines how to properly pass that to the underlying native installer. Details on the differences - http://stackoverflow.com/a/19777121 See More
The community repository contains multiple packages with similar names, making it hard to know which one to install. This is of course only related to using Chocolatey with the community repository, and you can look up the number of downloads to see which are the most widely used. See More
While Chocolatey seems to have a huge selection of packages including some windows updates, Scoop has a much smaller selection mainly focused on command-line tools. However, it can be argued that Scoop is focusing on a different type of setup than Chocolatey so package count may not be a good comparison. See More
Installs apps to their default locations, using your PC's language or one you choose, using Internet Explorer's proxy settings (so you can quickly get Chrome, Firefox, or Opera up and running on a fresh Window install). See More
Ninite makes sure that you've downloaded the right file, and that it's not corrupted, by checking the file checksums for each application. This means that you're less likely to end up with a buggy app, or to accidentally download malware/viruses, all with no extra work. See More
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