What would be the best format to encode in for animations which come out of Apple Motion? The animations consist of photos mixed with some png animations and motion effects. The file will be streamed to customers computers, and I don't know what kind of computer everyone will have. From what I read so far Flash is said to have the best in compatibility and convenience, but I don't know about the quality expecially coming out of Motion with effects and text. WMV seems to be a good option, however the quality of my encodes don't seem to be as good as Quicktime. I haven't read good things about streaming in Quicktime, and it also takes the longest to encode. The programs I own are Episode without the Flash option right now, and Compressor 1.2.
If you want to use Flash you really should buy the Flash 8 (On2 VP6) option for Episode. Flash 7 (Spark) will not look good at the same data rate.
Windows Media out of Episode should look in the same ball park as Quicktime. Make sure you're encoding to Windows Media 9. Make sure you've updated to Episode 4.2.2 btw.
Quicktime will look good if you use H.264 but the user must have Quicktime 7 to play the file back. Many PC users, especially in the corporate environments, don't have Quicktime 7. Both Compressor and Episode can do H.264 but Compressor 1.2 may not have all the features the current Compressor 2.3 has. You may want to upgrade your Final Cut Studio package while they still have the bargain upgrade price.
Also when you say "streamed" you REALLY need to know whether they'll be serving it on a true streaming server or http. Encoding for streaming server requires different parameters (depending on the codec) than http "progressive download" (which people often call "streaming"). You may get better quality on your encodes with motion graphics source if you're doing 2 pass VBR encodes for http progressive download.