I usually go with “not the sharpest knife in the drawer”. But then, I’m less imaginative than … I can’t think of anything.
A Canadianism:
“He’s playing hockey with a warped puck.”
Not the sharpest penny in the park.
That came out of my mouth one day at the park when I was very brain-dead (I was referring to myself). We’ve used it since, you should see the looks you get. 
Strong as an ox and twice as smart.
He rode the short bus to school.
I also like to mix up the standards, such as “the knife doesn’t go to the top floor” and “one light bulb short of a six pack”.
For someone with even more serious problems: “Crazy as a rat on acid.”
“Dumber than a ditch carp”
Actually, it’s “a boy that’s never played baseball.”
Shakes head. That boy’s as thick as a whale sandwich.
“Two coupons short of the toaster.”
Fifty responses in and nobody’s mentioned “couldn’t find his own ass with both hands (…and a mirror) (…and a road map) (…and a flashlight)” yet? All right!
He’s (in air quotes) special.
He rides the baby bus.
He freakin’ drives the short bus.
She’s pretty (said like the Southern “Bless her heart”)
Lights are on, but nobody’s home.
Not walking with the other ducks.
Oh yeah! and what about “wouldn’t be able to find his head if it wasn’t bolted on”??
Alternatively: “shithouse rat.”
Doesn’t know babyshit from butterscotch.
Not our Butterscotch mind you, just butterscotch in general.
Coupla’ destroyers short of a battle group.
Couldn’t find his ass with both hands and a GPS unit.
I also have been fond of saying “he/she can’t walk and breathe at the same time without passing out.”
Thanks for clearing that up! 
I love this one…
S/he couldn’t dump pee out of a boot with intructions written on the sole…
FML