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On one of my websites I have a photo gallery that requires the filename extension of the pictures to be in lowercase. Whilst it would be possible to recode the gallery code so that it could try different case extensions it's cleaner to just convert the filenames before uploading them to the website. On linux this is fairly straightforward using the rename command as follows.
rename -v 's/\.JPG$/\.jpg/' *.JPG
For more information see the rename man page.
Renaming the files is not quite as easy in Windows, but I've recently found a freeware program called A.F.5 Rename your files, which makes it possible. The program is free, but not open source. It has a lot of different options which allow for quite complex renaming of files, but the feature that I used was just to change the case of the filename.