Podcasters may not be aware of why they should not be posting video podcasts in the .mov format. .mov is a software “wrapper” that contains a minimum of two components: video and audio. The components can be in different codecs. So even if you believe that you are doing the right thing by using H.264 and AAC (you are), there are implications in using the .mov wrapper that you should be aware of.
.mov cannot be tagged. Well, a number of tags can be assigned in iTunes (notable exception being album art) but this only writes the tags to the database, not the file. This means that as soon as the episode is moved out of iTunes, it loses all the tags. In the case of podcasts, this includes, most tragically, the podcast flag and the long description. The only “tag” remaining is the title name and the disc and track number (if set), and this is only stored in the form of the file name. When you bring those episodes back into iTunes, they appear in the Movies library as 01 Episode 1.mov, etc, with no other tags. All that hard work from your RSS feed is wasted and is not recoverable.
A podcastee may have archived past episodes and want to reconstitute them into iTunes, or, as I have done in the past, handed them on to others so that they don’t have to download the episodes themselves. This saves lots of bandwidth. In either case, the results will be disappointing.
The MPEG 4 file format (.m4v or .mp4) is a wonderland of tagging possibilities. Cali and Neal, of Geekbrief.tv, for example, have recently started using one of my favourite tools, Lostify, to tag their .m4v (H.264/AAC) files as TV Show so that, in addition to all the embedded podcast tagging that iTunes does when the file is downloaded, they can be found in both the Podcasts and TV Shows libraries. Copyright, explicit, short description, etc. can also be tagged.
So my appeal to podcasters is to be aware of this and not to use .mov. The software you are using to create your files might be able to generate .m4v files. iMovie 08 will do it. Personally, I use QuickTime Player Pro to export MPEG 4 video (MPEG 4 or H.264) from .mov to MPEG 4 with the Passthrough option for both video and audio. This preserves the full quality of both components but regenerates them as a .mp4 file, the name of which is simply changed to .m4v prior to tagging (if H.264).