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actually an imlementation/porting of ajax file manager
http://www.phpletter.com/Demo/Ajax-File--Manager/would be great! I'm using it for a cms application developing for my company and its very powerfull.
Can be integrated with fck editor, has list or thumbnails view and filesmultiselect, can create folders,edit pictures(crop,resize etc), and last but not least its free :).
The best practice for organizing images and files I think, is through (any) filemanager. Uploading everything in the respective folders (uploads/...), and then when you need to add a file or an image somewhere, call the filemanager again, and just select the file/files that you need.
It needs a bit work to be fully integrated with XOOPS and lots of module developers will have to change their code but i think in the end XOOPS will be very powerful in organizing files. :)