For general video stuff I do I often lean on the H.264 codec as it tends to produce high quality at relatively small file sizes for most standard video stuff, however it is not always the best choice for everything, including using for video in Pro Tools post sessions. Randy Coppinger has written about some of the issues he has come across with the H.264 codec in Pro Tools. One of the trade-offs with using the H.264 codec is that because it uses a variable bit rate it can make your processing work harder as it needs to think a bit more about how to render the images. Randy Coppinger discusses that and more in another blog post.
I was given a movie that uses the related “AVC Coding” the other day and it didn’t play nice in Pro Tools (using v10 for most things at the moment) so I thought I’d transcode it to a different codec using MPEG Streamclip (an awesome app). Video codec choices can be a bit intimidating for poor audio folk like myself, so I thought I’d see what Avid’s recommended codec is for use in Pro Tools is and they promote their DNxHD codec as the recommended choice. It is not that standard on people’s systems though, so you can download it from here if you want to use it in MPEG Streamclip etc.
So in summary, consider using the DNxHD codec for videos in Pro Tools. It isn’t that hard for people to supply files in that format, or else to transcode prior to importing into Pro Tools.
Word of warning though, and that is that if you use MPEG Streamclip to convert to DNxHD the default settings make for a huge file size. Refer to this link for details on how to choose appropriate settings.