This ECMAScript can be integrated with the importScript(); feature for uploads with a chosen chunk size. It avoids some Upload Stash oddities not yet handled by the Upload Wizard.
VicuñaUploader is a free tool written in Java designed to upload files to Wikimedia Commons and other Wikimedia projects. It is a bit similar to Commonist but has some more functionality and different user interface.
ComeOn! is a free tool written in Java to upload pictures to Wikimedia Commons with extended support for JPEG metadata and its use in page templates. It is currently in beta mode but stable.
A free Android app is available for uploading images directly to Commons. (Android 2.3+ operating system required). The tool can be found on Google Play. You may adapt it for your own purposes using the GNU-GPL-licensed source code from GitHub.
Upload to Commons with iOS
An iOS app is also available on the AppStore. The source code is on GitHub under the Apache License.
Transfer tools
Uploading from Flickr
There are various tools to help upload files from Flickr.
F2ComButton - A tool which adds buttons to Flickr to easily upload images yourself or using Magnus's tool.
Flinfo - For people who want to upload Flickr pictures by themselves.
Upload Wizard - If you are an administrator or image reviewer, you can import images and photosets from Flickr via the Upload Wizard.
Commons Helper
This page will generate code that you can copy and paste when moving an image from a Wikipedia to Commons. Note that you still need to verify the source and only transfer images that have reasonable licenses. You also still need to give the image a category, although the assistant is hooked up to CommonSense, so it can suggest them at the same time. Developed by User:Magnus Manske.
Provided that you have the upload_by_url right, you'll see an additional input box on Special:Upload for selecting the upload source.
User's with the upload_by_url right (Image reviewers, Admins, GWToolset users), can directly transfer images from whitelisted websites via the API or via Special:Upload. With the Upload Wizard it is possible to upload files from Flickr.
Internet Archive
IA-upload is available for everyone (uses OAuth). You can select any Internet Archive free book, the description is prefilled and you are given a chance to edit it before upload.
If the desired book is not yet on Internet Archive, you can use BUB (Book Uploader Bot) to request its addition from another source. The job is entirely automatical, accepts requests for multiple books at once and can notify by email when the book is ready, with a link to ia-upload to complete the transfer.
Internet Archive also provides conversion of video from any format to ogv. You are advised to upload the video at the highest quality you have, up to about 400 GB per item.
Ivideo2commons is available for everyone (uses OAuth). You can select any video on the web and upload it. The tools is automatically converting the video to a commons compatible format.