gistfile1.sh

#!/bin/bash
#
# Links files in this directory to the current users home directory.
#
# If the link already exists the file will be skipped unless the -f flag is given.

real_path () {
    _=`pwd`
    [ -d $DIR ] && DIR=$1
    [ -f $DIR ] && DIR=`dirname $1`
    cd $DIR && echo `pwd` && cd $_
}

SCRIPT_DIR=$(real_path $0)
SCRIPT_PATH=${SCRIPT_DIR}/`basename $0`
FORCE=0
PREFIX=$HOME

while getopts "fp:" flag; do
	case "$flag" in
		f) FORCE=1 ;;
		p) PREFIX=$OPTARG ;;
	esac
done

PREFIX=${PREFIX%/}

for FILE_PATH in ${SCRIPT_DIR}/*; do
	FILE=$(basename $FILE_PATH)
	HOME_PATH=$PREFIX/.${FILE}

	if [[ $FILE_PATH = $SCRIPT_PATH ]]; then
		continue
	fi

	if [[ $FILE_PATH = $SCRIPT_PATH || ${FILE:0:1} = '.' ]]; then
		continue
	fi

	if [[ $FORCE -eq 0 && -e $HOME_PATH ]]; then
		echo Skipping $FILE_PATH
		continue
	fi

	if [[ $FORCE -eq 1 && -e $HOME_PATH ]]; then
		echo Forcably linking $FILE_PATH to $HOME_PATH
		rm -f $HOME_PATH
	else
		echo Linking $FILE_PATH to $HOME_PATH
	fi

	ln -s $FILE_PATH $HOME_PATH
done

Instead of checking FILE_PATH against SCRIPT_DIR, you can use find -mindepth 1. Though since you use -maxdepth 1, why not:

for FILE_PATH in ${SCRIPT_DIR}/*; do

Beware if you run this on a non-GNU setup: -mindepth/-maxdepth are GNU find extensions.

@rdpate oh but that makes too much sense... can't have that now! (thanks for the tip!)
@mrc I have -mindepth/-maxdepth on BSD find (OSX 10.6).

@jlogsdon That's lucky (I didn't know about BSD find on OSX). But it's not required by POSIX, and isn't found in some recalcitrant Unixen - for example, it's not in Solaris 10, which is a problem for, um, me :-) (but maybe it's just me!)

@mrc that's good to know! Fortunately, for FILE_PATH in ${SCRIPT_DIR}/* works just as well as @rdpate pointed out.