If you are comfortable with a command line solution, you could do something like this, in bash

i=1

for file in *.*; do

  printf -v newfile "%03d.%s" $((i++)) ${file##*.}

  echo mv -v -- "$file" "$newfile"

done

The echo will prevent it from actually making any changes (it will just output a list of mv commands that it would make) - you can actually make the changes by running the same command without the echo once you are satisfied that it's going to do what you want.