I am looking for the same answer on video but do have a comment on audio.
For me I want the best possible quality, space is not an issue especially for music. What I have found is that the AIFF and WAV formats are uncompressed and maintain the best possible quality. Itunes, JRiver, and my Ipod and Iphone all play the AIFF format. And I am pleased, I believe all play the WAV format as well. Itunes will let you rip from CD to AIFF and it is fast because there is no compression. I have also learned that the FLAC format maintains the original PCM quality of AIFF and WAV but is Lossless and therefore has the same quality but takes less space, it is compressed. The Apple Lossles fromat is similar to this as well. Unfortunately, Itunes and Ipod do not support the FLAC format. This is not a big issue in general unless you want some of the new HD music that is being produced from Companies like HDTRacks. They obtain HD music, like an old album that has been remastered and put out in 192 mhz vs. normal 44 mhz on CDs. They provide these in FLAC format only, which is a bummer, for the itunes and Ipod people.
So best quality AIFF or WAV - FLAC and Appleloss less if you want same quality but less space - but device playability issues.
What have you learned if anything on Video format - I want the same thing I want the highest Quality - I use M2TS for Blu-Ray but ISO for DVD. THe problem I am having is that JRiver will play an ISO but it has to be virtually mounted. I want to put the ISOs in the Library without having to mount it. If you mount it, then import to the library it works - but if you unmount it it breaks the library link. The problem with virtual mounting is that you can only do what drive letters are available so like G-Z. But I have hundreds of ISO files. I have heard something about H.264 and MPEG 2 but I am having a hard time discerning what is best quality, again space is not an issue. ISOs are great but I want convenience in my library. ISOs play fine on my WDLive media player, I just love the JRiver interface though.
Hope this helps and you can help me as well.