I am currently using the newest version of Adobe CC and have a casino client that has me making animations for their many LED boards across a few different platforms. These LED screens, come in a variety of sizes, 1920 X 1080 / 580 X 452 / 720 X 1280. Unfortunately, only 80% of these things take .mp4s. The other 20% use WMVs. I know about Flip4Mac, but I do not think it lets you do whatever resolution you want. If I remember correctly, they have a set list of approved resolutions. Does anybody know of a software that can encode into these weird sizes from .MOV or .MP4?
FFMPEG is one good way to go. You will most likely need to use it via terminal, but it's very powerful and one of the most tolerant of things which *should* work but are not commonly used, like odd frame sizes (or frame rates, for that matter).
I've also experienced embedded WMV-only playback devices being very picky about the flavour of WMV you give then. FFMPEG will give you decent control over that, too, though it will take some learning of the intricacies of a not-so-simple command line tool.
More generally, FFMPEG is a great Swiss-Army-knife for encoding and decoding all sorts of exotic codecs and formats. Lots of apps are built on top of it, but I like to use the terminal version for the more challenging tasks ... it's slower than click-n-drag, but you get a lot of fine control. The only downer: I haven't had much luck with GPU acceleration on the Mac, so any heavy lifting transcoding goes via other apps.