Advice for a low-loss intermediate video format?

[jemenake]

Okay, here's the quick synopsis:
1) I use Handbrake almost exclusively for converting vids to H264/AAC for my iPad/iPhone.
2) I've got a set of MPG videos which I want to convert, but, on most of them, Handbrake complains that "No Title(s) found. Source may be copy protected, badly mastered, yadda yadda yadda..."

But they play fine on VLC. So, I know that the audio and video are there, but Handbrake is just getting confused. So, I want to convert these to an intermediate format which Handbrake can deal with.

My first crack at it was to use mencoder to just convert it to a basic AVI:
mencoder input.mpg -o output.avi -of avi -oac copy -ovc lavc -lavcopts vcodec=mjpeg:vbitrate=1000

I picked mjpeg because I figured it would be a little less lossy than other codecs (I might switch to ljpeg). Handbrake deals with the resulting file just fine. But, because I've got quite a few of these to convert, I figured I'd ask:

What video codec would you suggest as an intermediate format? Because it's temporary, file size isn't an issue. What I'm after, primarily, is 1) fast encoding and 2) minimal loss of video quality from the extra encoding.

I've got access to Handbrake, mencoder, ffmpeg, and vlc/cvlc. Suggestions?

P.S. Yeah, I've tried just using cvlc and ffmpeg to convert straight to the H264/AAC, but one of the ended up producing videos where iTunes/iPad/iPhone couldn't play the audio (although VLC, as always, played it fine), and I don't remember what went wrong with the other program. So, I'm kinda fixated on Handbrake for rendering the final product.

[Baldrick]

I would use a lossless codec like huffyuv ( http://www.mplayerhq.hu/DOCS/HTML/en/menc-feat-enc-libavcodec.html ).