…that possibly go back generations.
Dad (knocking on the bathroom door): “You fall in?”
My mom used this word I copy – it means something like flummoxed/bewildered but sounds like fuhrhunnuxed. It must be Pennsylvania German but I haven’t been able to find anything but ferdoodled. I keep using it because it sounds like what it is. 
My Mom, complaining about someone being slow and holding everyone else up:
“C’mon, you’re moving like dead flies are falling off you!”
I guess faster moving people have live flies fallng off them instead or something?
None of these phrases are original to my parents, but I learned them from my parents, so I think they fall into your category.
Dad – “Now you’re cooking with gas.”, “Everything copacetic?”, “Dark green.” (Dark green referred to something really cool.)
Mom – “Naughty naughty.” – Mom would say this when we, as young kids, did something more or less correctly, when we could more likely have done them badly. It was her way of saying kids will be kids. (Once we turned 18 this was replaced with “You know better than that!”)
And one that I think was specific to Uncle Don – “Are your fingernails clean?” – His way of saying “Stay out of trouble.”
My mother (age 91) says of a really good guy, “He’s true blue and a yard wide.”
My late husband (would have been 77 this year) had a word like what gigi described above, “bumfuzzled.”
Also, if someone was really confused, he’d say, “They don’t know whether to shit or go blind.”
A family expression I have rarely used is “The things you see when you don’t have a gun.”
The way my father told us to get lost was, “Run around the corner and see if it is raining”. I have used it occasionally. I think it was original with him.
A friend told me that his father would say, "Go tell your mother that she needs you [maybe it was “wants you”].
This isn’t nearly as archaic as some of the phrases, but my mom always describes things as “Neat.” So I will do the same.
It’s amazing how many people comment over the fact that I use “neat” to describe something. Maybe it’s a younger generational thing, but I can think of 3 people off the top of my head who have made a comment about it in the last, oh, 10 years or so.
My Dad, if asked to do something by us kids when he was busy or tired: “I can’t, I’ve got a bone in my leg”.
Well, so you do, so you do. Now if you didn’t…
“Wolf, are you there?” when calling in at somebody’s place or as a conversation opener.
The word Ochoa in our family name means wolf.
“First of all, know your people”. This one is a cultural slogan (it might count as a shibboleth), but damn if it ain’t true. Outsiders will ask “first what?” “First rule of management, first point of business, first thing you have to do… how the hell would you get anything done, if you don’t know your people? 
”
I’m always confused when a new manager, or a manager who’s getting a new subordinate and wasn’t the hiring manager, doesn’t make it a Point to meet them ASAP.
My dad wasn’t one to dwell on things outside his control. If one of us kids complained about something that wasn’t ever going to change, Dad would often remind us, “If a frog had wings, he wouldn’t bump his ass.”
I use this phrase at every opportunity. I gave the eulogy for my dad last year. I built it around this phrase.
Might it have been farmissht ? That’s a Yiddish word heard around my house quite frequently growing up. Heck, if Yiddish expressions count I’ve got a ton of them and find myself met with confused stares whenever I use them.
My Dad used to say “better he should owe it to you than cheat you out of it”. Always seemed to me that I wasn’t getting “it” back either way. Also heard " she is the cat’s mother" as discussed in another thread.
Not my parents, but my grandmother: Beauty’s only skin deep, but ugly’s to the bone.
“read a book” in reply to me being bored
“never say never” in reply to something like “you never let me ___________”
cant think of any others
God, last week I found myself sighing at my 19 month old and saying “CHILD of GRACE…”
It’s like my mother just came out of my mouth. I have no idea how it happened. It’s happen twice since then!
I copy my dad on purpose, when somebody goes to the kitchen say to get a beer or something, “Those come like dead men in a casket?” (Meaning one at a time, or are you gonna ask if I want one?!)
My grandma said “run around the corner and see if it’s raining”, too. Also “go play tiddlywinks with manhole covers”, which I have never really known what tiddlywinks is except that it’s a game old people used to play, presumably not with manhole covers.
“Don’t just sit there like a bump on a log.”
“Eat it or wear it.”
I’ve translated it from German for you. “It’s better than having someone shit in the open palm of your hand.” Roughly means “better than nothing.”
My mother, when she is at the end of her rope and has completely run out of patience for someone/something, has been known to declare “I have had the weinie!”
For reasons of my own mental health, I have elected not to examine that particular exclamation closely. On the other hand, I’ve been known to use it myself on occasion.
When my mom is startled or exasperated, she’ll often exclaim, “Jesus Mary and Joseph!” I use that one once in a while now, usually when I’m at my wits’ end rather than when I’m startled. I’ll shake my head and mutter it under my breath when my kids have just destroyed something.