What output formats do you encode to?
H.264 is currently the highest quality video codec available, which means that it can usually look better at the same file size, or the same at smaller file sizes, than other codecs. It's also widely deployed, and most web browsers can play it (either natively, or via a Flash plugin), and so can many mobile devices, like the iPhone and Android. But there are licensing issues to consider.
Theora is a free and open video codec with no licensing issues. It is natively playable in many browsers, including Firefox, Chrome, and Safari. But compression is a bit worse than H.264.
VP8 is a newer codec. Like Theora, it is free and open. But it compresses better than Theora, and about as well as the H.264 Baseline profile. H.264 is still better in its Main and High profiles. But that will hopefully change as VP8, and VP8 encoders, mature. VP8 is expected to be widely adopted in web browsers, and can be played today in the newest versions of Chrome, Firefox, and Opera.
VP6 is supported natively in Flash 8, and so is widely used on the web. It is a good codec, but doesn't compress as well as H.264. We encode to VP6 in the FLV container, with MP3 audio.
MPEG-4 is often used in a 3GP format on mobile devices.
WMV is a Windows codec. We specifically support WMV 8, which is confusingly the same as WMV2.
MP3 is a pretty good audio compression format. But you do have to pay royalties on distribution of MP3 content in some cases.
AAC is quite similar to MP3. The standard itself is better, but MP3 encoders are often a bit more mature, so the quality differences between them are small. There are no licensing fees for distributing AAC content.
Vorbis audio is free and open, just like Theora and VP8 for video. Vorbis is a good audio codec, and is very comparable to MP3 or AAC.
WMA is a Windows audio codec that we support alongside of WMV video.
Microsoft Smooth Streaming (MSS) is an adaptive bitrate format which enables streaming of video content to platforms such as Microsoft Silverlight, XBox 360, Windows Phone 7, and select connected TV platforms.