This has always been an interesting idea that many people have tried to figure out how to do...but it always comes down to the same thing, and that is when you get into called shots, people will want to call a shot to the neck. Needless to say, smacking someone with an arrow right in the neck or chopping it off with a sword will doubtlessly lead to death, and this is generally very unbalanced.
What I'd say is that you can't call a shot to such a body part. The way I think about it is that you aim for their heart, throat, whatever, but they try to dodge. Sometimes they're successful, sometimes not, and sometimes you jsut miss, but because of these changes you don't really hit where you were aiming. The true strike to a vital area is the final blow.
Now if you have someone tied up, I'd say you can pretty much just let them do whatever. No tongue means no talking, having a loss of fingers could probably give you penalties to attacking, manual skills, and a certain percent on somatic components for spell failure.
One leg, I'd say reduce their speed to 5ft. while prone, or 10ft. while standing, but every round they have to make a balance check (more if they're moving) or fall prone.
You can just wing stuff like that.
I'm pretty sure someone came up with a table of "creative criticals" which basically damages parts of the body on critical hits...I always found it to take too much time, but it is an intersting set of rules.