My Script:

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#!/bin/bash

STRIPPED=${1%.*}

ffmpeg -i $1 -an -pass 1 -s 576x432 -vcodec h264 -b 300k -flags +loop -cmp +chroma -partitions 0 -me epzs -subq 1 -trellis 0 -refs 1 -coder 0 -me_range 16 -g 250 -keyint_min 25 -sc_threshold 40 -i_qfactor 0.71 -bt 300k -maxrate 350k -bufsize 2M -rc_eq 'blurCplx^(1-qComp)' -qcomp 0.6 -qmin 10 -qmax 51 -qdiff 4 -level 13  $STRIPPED.mp4

rm $STRIPPED.mp4

ffmpeg -i $1 -acodec libfaac -ab 32k -pass 2 -s 576x432 -vcodec h264 -b 300k -flags +loop -cmp +chroma -partitions +parti4x4+partp4x4+partp8x8+partb8x8 -flags2 +mixed_refs -me umh -subq 7 -trellis 2 -refs 5 -coder 0 -me_range 16 -g 250 -keyint_min 25 -sc_threshold 40 -i_qfactor 0.71 -bt 300k -maxrate 350k -bufsize 2M -rc_eq 'blurCplx^(1-qComp)' -qcomp 0.6 -qmin 10 -qmax 51 -qdiff 4 -level 13 $STRIPPED.mp4
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Output:

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FFmpeg version SVN-r9450, Copyright (c) 2000-2007 Fabrice Bellard, et al.
  configuration: --enable-shared --enable-gpl --enable-libfaac --enable-libx264
  libavutil version: 49.4.1
  libavcodec version: 51.40.4
  libavformat version: 51.12.1
  built on Jun 29 2007 22:08:29, gcc: 3.4.6 20060404 (Red Hat 3.4.6-8)
[NULL @ 0xb71370]looks like this file was encoded with (divx4/(old)xvid/opendivx) -> forcing low_delay flag
Input #0, avi, from '0512-Mitchell.avi':
  Duration: 01:31:36.1, start: 0.000000, bitrate: 1071 kb/s
  Stream #0.0: Video: mpeg4, yuv420p, 640x480,  2.00 fps(r)
  Stream #0.1: Audio: mp3, 44100 Hz, stereo, 112 kb/s
Output #0, mp4, to '0512-Mitchell.mp4':
  Stream #0.0: Video: libx264, yuv420p, 576x432, q=10-51, pass 1, 300 kb/s,  2.00 fps(c)
Stream mapping:
  Stream #0.0 -> #0.0
[libx264 @ 0xb71370]using SAR=1/1
[libx264 @ 0xb71370]frame MB size (36x27) > level limit (396)
[libx264 @ 0xb71370]using cpu capabilities: MMX MMXEXT SSE SSE2
Press [q] to stop encoding
[mpeg4 @ 0xb71370]looks like this file was encoded with (divx4/(old)xvid/opendivx) -> forcing low_delay flag
[mpeg4 @ 0xb71370]looks like this file was encoded with (divx4/(old)xvid/opendivx) -> forcing low_delay flag
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