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Pros
Pro Handles updates for you
Save yourself from having to manually update all those small apps that don't auto-update themselves.
Pro Well adapted to the Windows environment
Pro Install in bulk, without the restarts
Perfect for getting a fresh install of Window up to speed in as little time as possible.
Pro No toolbars or extra junk
Ninite's installation does not install "extra features" offered during installation.
Pro Saves you from manually filling in all the details of installation
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).
Pro Curated list of commonly used quality software
Everything from Steam and iTunes to Putty and Eclipse - likely has most, if not all of the major free applications you use on a regular basis. Check the website for the full list.
Pro Verifies file checksums
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.
Cons
Con Limited selection of apps
Con Installs apps only in their default location
Very unfortunate for those having their system on a budget or even mid-tier SSD.