I think these are the ones listed in Tools --> Preferences --> File Handling --> Converters (see screenshot at the bottom). There you can see the command line arguments used.
$$<letter> variables refer to the following (from the LyX Customization manual, found under Help --> Customization, section 3.3):
$$s The LyX system directory
$$i The input file
$$o The output file
$$b The base filename of the input file (i.e., without the extension)
$$p The path to the input file
$$r The path to the original input file (this is different from
$$p when a chain of converters is called)
$$e The iconv name for the encoding of the document.
Quoting the manual mentioned above:
In the Extra Flag field you can enter the following flags,
separated by commas:
latex This converter runs some form of LaTeX. This will make LyX's LaTeX error logs available.
needaux Needs the LaTeX
.aux file for the conversion.
xml Output is XML.
The following three flags are not really flags at all because they
take an argument in the key = value format:
parselog If set, the converter's standard error will be redirected to a file
infile.out, and the script given as argument
will be run as:
script < infile.out > infile.log. The argument may contain `$$s`.
resultdir The name of the directory in which the converter will dump the generated files. LyX will not create this directory, and it
does not copy anything into it, though it will copy this directory to
the destination. The argument may contain
$$b, which will be
replaced by the base name of the input and output files, respectively,
when the directory is copied. Note that
make no sense together. The latter will be ignored if the former is
resultfile Determines the output file name and may, contain
$$b. Sensible only with
resultdir and optional even then; if not
given, it defaults to