simple bash script to replace non-alphanumerics with underscores, probably written a million times before this.

underscorify.sh

#!/bin/bash

# examine all files names in current directory and emit a 'mv' command to rename
# if the filename has non alphanumeric in it, other than dot or underscore

# first loop  all files, could use find for this, since loop isn'te recursive

for f in *.*; do 
  # if filename has bad chars 
  if [[ $f =~ [^a-zA-Z0-9_\.] ]]; then
     # create new filename with underscores, remove double underscores
     newf=`sed 's/[^a-zA-Z0-9_\.]/_/g' <<< $f | sed 's/__/_/g'`
     # echo mv command
     echo "mv \"$f\" \"$newf\""
  fi
done

To use: save the above file in your path, then

 cd my/folder/with/badiflenames

 # test to see if you like results
 underscorify.sh |less
 # run the emitted 'mv' commands
 underscorify.sh | bash
 # test that all files were found 
 underscorify.sh   # should be blank