It took me some times to figure out how to handle the filenames. The secret is cygpath, which transforms cygwin filenames to windows (-w option) filenames

#!/bin/bash
DIR=$(cygpath -w $(pwd))
DEST=$DIR/png_$1
mkdir $DEST
INKSCAPE="C:/Documents and Settings/monnier/Desktop/labo/LATEST/inkscape/inkscape.exe"
for i in $(ls *.svg) 
do
	"$INKSCAPE" $DIR/$i -e ${DEST}/${i}_${1}.png -w $1
done