Using ffmpeg to convert to Photo Jpeg with minimal loss of quality
DNxHD and JPEG are not the only game in town as far as intermediate codecs are concerned (intermediate codecs being high-quality, visually lossless codecs designed for moving media between steps in a post-production chain). Probably the most-used intermediate codec is Apple's prores 422, which can be encoded cross platform using ffmpeg thus:

ffmpeg -i uncompressed.mov -c:v prores -profile:v 3 -c:a pcm_s16le output.mov


One of the biggest advantages of prores is the support for 10-bit encoding, giving you much better colour fidelity. You can also use the prores 4444 variation to avoid chroma subsampling (reduction of the colour resolution) and alpha channel support.

Failing that you can use motion-JPEG, or even 2 flavours of lossless JPEG (I have no idea what the difference is). Oh and there's JPEG2000 if you really want, though it's not recommended. Substitute your codec of choice here:

ffmpeg -i uncompressed.mov -c:v CODEC -c:a pcm_s16le output.mov


where CODEC is one of:


jpegls - lossless JPEG (?)
ljpeg - another lossless JPEG (?)
mjpeg - motion JPEG
jpeg2000 - JPEG 2000


Since you're on linux I won't suggest Cineform, it's a good intermediate codec on win/mac but I don't think there's a CFHD codec for linux yet, and ffmpeg can only decode it (it's been open-sourced so that will probably change). There are a couple of more obscure ones like Grass Valley, huffyUV, dirac and so on, but if you can't use DNxHD it's unlikely these will be any use to you. Just as an aside, DNxHD is freely available from Avid, is it possible to install the codec on the target machine?