If you're dabbling in video these days, you've probably been using a DSLR. Nikon and Canon have both made a big push into the market with the hopes of enticing a new generation of filmmakers, offering video modes on their pro and entry level models. Considering the relatively low price, the results are impressive, making great films possible on even modest budgets.
Motion JPEG is one of the oldest video formats still in use today, most commonly found in digital cameras and other video-capable devices. Unlike MPEG or h.264 formats, M-JPEG takes a very different approach to video compression. Instead of compressing the entire video as a whole, each frame is compressed as an independent JPEG image, and strung together into a coherent video sequence.
However, there is one big trade off. Encoding each frame as its own image means that file sizes can be huge, often twice as large as other compressed video formats. This is because the format has a relatively high bit-rate, but no compression outside of the JPEG standard.
Technically, this means that the quality of an h.264 encoded video is actually less than that of M-JPEG. However, in practice, the difference is almost imperceptible to the end-user, making the the tradeoff in size more than worth it.
If you're concerned about storage, and don't have flash memory to waste, h.264 encoded video is your best bet. You'll be able to store more video at a time, and hardly notice a difference in terms of quality or compression. However, if you want to be sure you're getting the best in picture quality, M-JPEG should suit you fine. As an older format, it's more widely supported across platforms, and requires less processing power to both encode and decode too. But it's also very greedy in terms of space, so be sure to watch those memory cards.
Image via Flickr user scolirk, alax.info and Wikipedia.