Here's a script (originally by Toby White) that I hacked up to compare the entire directory structure in FileMerge rather than opening each file individually.
#!/bin/sh
#
# This script was written by Toby White under an unknown license, and published
# on the Git mailing list:
#
#   http://kerneltrap.org/mailarchive/git/2007/11/21/435536
#
# Superficial changes were made by Nathan de Vries to allow the script to be
# run under Leopard.
#
# Adapted by Daniel Miller : http://stackoverflow.com/a/12957945/10840
# - allow changes to be saved back to the working copy when diffing against HEAD
# - work when FileMerge is already open
# - always compare archived copies so ignored files are excluded from the diff
# - allow diff of unstaged changes (no arguments); creates a dangling commit
# - allow diff of subdirectory within the repo
#
# Known issues:
# - Always uses the same two directories (/tmp/git-opendiff-old and
#   /tmp/git-opendiff-new); THEY WILL BE DELETED IF THEY ALREADY EXIST.
#   Ugly, I know, but it makes the script work even if FileMerge is open.
OLD=
NEW=
FILEPATH=
HAS_ARGS=no
IGNORE_TO_PATH=no
# loosely based on https://stackoverflow.com/a/14787208/10840
while [ "$#" -ge 1 ]; do
    HAS_ARGS=yes
    case "$1" in
        -h)
            echo "usage: $0 [--cached | <ref> [<ref>]] [-- <path>]"
            exit 0
            ;;
        --cached)
            # diff staged changes
            NEW=$(git write-tree)
            OLD=HEAD
            IGNORE_TO_PATH=yes
            shift
            ;;
        --)
            shift
            FILEPATH="$@"
            break
            ;;
        *)
            if [[ "$IGNORE_TO_PATH" == "no" ]]; then
                if [ -z "$OLD" ]; then
                    OLD="$1"
                else
                    NEW="$1"
                    IGNORE_TO_PATH=yes
                fi
            fi
            shift
            ;;
    esac
done
if [ -z "$OLD" ]; then
    OLD=HEAD
fi
if [[ "$HAS_ARGS" == "no" ]]; then
    # diff unstaged changes
    # http://stackoverflow.com/a/12010656/10840
    NEW=$(git stash create)
    echo "diff unstaged changes"
fi
TMP_OLD=/tmp/git-opendiff-old
TMP_NEW=/tmp/git-opendiff-new
test -d $TMP_OLD && rm -rf $TMP_OLD; mkdir $TMP_OLD
test -d $TMP_NEW && rm -rf $TMP_NEW; mkdir $TMP_NEW
TMP_OLD=$TMP_OLD/$OLD; mkdir -p $TMP_OLD
git archive --format=tar $OLD $FILEPATH | (cd $TMP_OLD; tar xf -)
if test -z "$NEW"; then
    SAVE_TO=$(git rev-parse --show-cdup)
    test -z "$cdup" && SAVE_TO=.
    git archive --format=tar HEAD $FILEPATH | (cd $TMP_NEW; tar xf -)
    opendiff $TMP_OLD/$FILEPATH $TMP_NEW/$FILEPATH -merge $SAVE_TO &> /dev/null &
else
    TMP_NEW=$TMP_NEW/$NEW; mkdir -p $TMP_NEW
    git archive --format=tar $NEW $FILEPATH | (cd $TMP_NEW; tar xf -)
    opendiff $TMP_OLD/$FILEPATH $TMP_NEW/$FILEPATH &> /dev/null &
fi
Put this somewhere on your path. I prefer ~/bin/git-opendiff, which means git opendiff ... works as expected.
Update: diff unstaged changes when called with no arguments, added -h (help) option.
Update: diff subdirectory with -- <path>. Also better argument parsing.