Run QuickTime from command line to export video

Checkout the video here:

How to Use Quicktime to Crop Video with Letterbox/Pillarbox

If you upgraded SL from Leopard you can do this via Quicktime 7 otherwise they have cut out all the awesome editing features from QT10. :(

This answer is hella long because your comments seem to indicate that your main interest is AppleScript itself, not converting videos from FLV to MP4. If this is the case, I strongly recommend starting with a good AppleScript reference, reading carefully and learning to use the tools available to you (especially Script Editor and application dictionaries). Trying to learn a new language by modifying existing applications is not good for debugging and can end in very bad things like cargo cult programming. That said,

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I'd start by opening QuickTime Player's dictionary (File->Open Dictionary... in Script Editor) to see what commands are available. In my version of QuickTime Player (7.6.4), there's an export command in the QuickTime Player Suite:

export v : Export a movie or track to a file

   export reference : the movie or track to export
   to file : the destination file
   as AIFF/Apple TV/AVI/BMP/DV stream/Fast Start QTVR Movie/FLC/hinted
      movie/image sequence/interframe compressed VR object movie/iPhone/
      iPhone cellular/iTunes/MuLaw/MPEG2/MPEG4/picture/QuickTime media
      link/QuickTime movie/QuickTime TeXML/standard MIDI/System 7 sound/
      text file/ThreeGPP/wave : the desired file type
   [using default settings/most recent settings] : the export settings
      to use
   [using settings preset string] : the name of the export settings
      preset to use
   [using settings file] : the file containing the export settings
   [replacing boolean] : should the original file be deleted first?

A little Googling suggests that the "iPhone" file type refers to a .m4v file, so a first step might be replacing save first document in target_path as ".m4v" with export first document to target_path as iPhone. Looking through the dictionary a little more, though, shows that there's also a can export command:

can export v : Determine if a movie or track can be exported to the desired
   type

   can export reference : the movie or track to export
      as AIFF/Apple TV/AVI/BMP/DV stream/Fast Start QTVR Movie/FLC/hinted
         movie/image sequence/interframe compressed VR object movie/iPhone/
         iPhone cellular/iTunes/MuLaw/MPEG2/MPEG4/picture/QuickTime media
         link/QuickTime movie/QuickTime TeXML/standard MIDI/System 7 sound/
         text file/ThreeGPP/wave : the desired file type
      → boolean : is the export supported

So we should check that it's possible to export the movie in iPhone/.m4v format before actually doing so:

if (can export first document as iPhone) then
   export first document to target_path as iPhone
else
   error "Cannot export " & (source_file as string) & " in .m4v (iPhone) format."
end if

If we stop here, though, we may notice that some of the output files don't play correctly beyond a certain point, because QuickTime can load files asynchronously (i.e., not all at once). We should try to check that QuickTime Player has finished loading a movie before we tell it to export; by examining the full list of load states listed in the dictionary and assuming that every movie eventually ends up in a finished state or an error state, we can add this relatively easily.

set error_states to {load state unknown, load error}
set successful_states to {loaded, complete}
repeat until load state of first document is in (error_states & successful_states)
   delay 0.1
end repeat

if (load state of first document is in successful_states) then
   if (can export first document as iPhone) then
      export first document to target_path as iPhone
   else
      error "Cannot export " & (source_file as string) & " in .m4v (iPhone) format."
   end if
else
   error "File is not in a successful load state: " & (load state of first document as string)
end if