Your best option is Quicktime Pro. It's exports are a bit slower, but the quality is great. You will have to pay, but it's very reasonable.
The cheapest good option is FFMPEGX - a great all-around video conversion program for your AVI and MPEG. FFMPEGX will convert just about anything.
50mb is probably overkill for a 4 minute music video, but if quality is that important to you, go ahead. However, your MPEG videos are poorly-compressed MPEG-1 video. Think 1997 here. A 4 minute music vid is what, about 40mb? Making it a 50mb .mov is not gonna ADD quality, just filesize.
i would suggest experimenting a little, and finding a bitrate that makes you comfortable. Then sticking to it for everything. If you want high quality, maybe go with 500k/s for the video, and 128k/s for the audio.
oh, and be sure NOT to change the resolution on all those AVI and MPEG files. They've already been resized once. Don't do it again.