Once you finish a project there are a lot of ways to output it. Compression is a vast & mysterious art so I will try to put up some starting points here to get you on your way.
Everytime you make a video you should make one master export that you save in a very safe place! You never know when you will want that footage again (grant application, work reel, etc.) and you never know what the standards will be when you get there so always export one version at the highest level you can - usually the same codec you shot in. In most cases this will be DV at 720x480.
For live image processing (Isadora & Jitter)
Codec should be photo - jpeg
320 x 240 (minimum)