whenever I encode .mov files with the H.264 codec, they always come out looking like, well like a first generation web video - ie like S$*T.
I did a quick test of an H.264 MOV earlier today for someone else; check it out here. This is PAL DV to H.264, at about 2Mbps; I think it looks OK. I can get much better from the MainConcept H.264 encoder, or an external encoder, but it's usable.
My best guess is that the profile is preset to use 'baseline' - if so, is there a way to change this? I can't find any options to change to change the profile, or levels, or anything with regards to H.264 - there is a "codec settings" button, but that is grayed out.
According to MediaInfo, the H.264 MOV generated by Premiere is actually using the Main profile; the Level varies based on frame size and where you limit the bitrate. You don't have a lot of options here because, well, I don't think Apple's/QuickTime's implementation of H.264 gives you many options. It's a pretty rotten encoder, at least in comparison to some of the other choices out there.
If you want more flexibility in creating an H.264 encode, use the H.264 format; it's in the same list as QuickTime. You'll have much more you can choose from and more flexibility when controlling your encode. It still doesn't give you as much control as, say Sorenson Squeeze (MainConcept codec) or x264 (open source H.264 encoder, which gives you even more than MainConcept), but you can get some decent looking encodes. The video will be put in an MP4 container, which will playback in QuickTime.
Do you need an MOV? If so, check out MPEG Streamclip. I'm assuming you're using Windows, so that's where the link goes; there's a Mac version as well, however. Anyway, MPEG Streamclip is my go-to gadget when I absolutely have to send an H.264 MOV. It's still using Apple's encoder, but it looks better, and you have a little more control. Just spit out an uncompressed file from Premiere (has to be an uncompressed AVI or else any kind of MOV) and encode from Streamclip--works a treat.