Example for the impatient: http://commons.wikimedia.org/wiki/Special:Commander?pane1=cat&cat1=Museums_in_Cambridge&run1=1&pane2=cat&cat2=Cambridge&run2=1&testing=1&withJS=MediaWiki:Commander.js (currently limited to Commons logged-in users only; tested in Chrome, Firefox, Safari; wide screen is advantageous...)
A complete rewrite of the toolserver demo, the new Commons Commander runs as JavaScript directly on Commons as a faux Special Page. All operations use the official API, so actions will be logged as if you had performed them manually. The given URL includes a test mode (discernable by the big "TEST MODE" in the page heading), so you can play without fear of breaking things. To use the "real thing", try: http://commons.wikimedia.org/wiki/Special:Commander?withJS=MediaWiki:Command...
Commander uses the namegiving Norton Commander two-pane view. Many functions of the old Commander have not been reimplemented yet, but the big ones are working: Browsing files (with "eternal scroll"), and adding files to categories. For the latter, is you have a category pane open, just drag files onto the category pane, done (except in test mode, of course). If you drag files from one category into another, you will move the files by default (remove them from the "source" category and add them to the "target" one). To just add ("copy"), keep the ALT key pressed. Just like you do with files on your computer.
You can select multiple files, then drag one of them to move/copy all. When you select files on a category pane, the parent- and sub-categories get copy- and move-functions to click (might become drag'n'drop later...).
There is more to come, like search and renaming files, but I'd like to share this early version with you.
To permanently add the Commander to your Commons experience, add
importScript('MediaWiki:Commander.js');
to your http://commons.wikimedia.org/wiki/Special:MyPage/vector.js page. That way, you also get toolbox links on user and category pages, to browse and organize the respective contents with the Commander.
For the geeks, source is here: http://toolserver.org/~magnus/commcomm/wpinclude.js (I could just copy it to Commons, but developing in a textarea is a pain...)
Cheers, Magnus
P.S.: As always, feedback is welcome!