3rd Rock From the Sun (CBS, 1996-2000) 

    "Dick is From Mars, Sally is From Venus", 30 January 1996
  Tommy Solomon (Joseph Gordon-Levitt), given the role of "teenager"
  in the alien group sent to Earth on a "research mission", starts going 
  to High School, and his teachers criticize Dick Solomon (John Lithgow),
  who takes the role of Tommy's father, for lack of discipline.
  Back at home, Dick, Tommy and Harry Solomon (French Stewart) are
  planning how Dick and Tommy can appear more like father and son.
  Harry says he has seen fathers doing this (he ruffles Tommy's hair),
  and Dick agrees and ruffles Tommy's hair himself.  Then Tommy
  stands up and ruffles Dick's hair.  Dick says, with delight, "Look, we're
  roughhousing!"

    "Father Knows Dick", 7 May 1996
  Dick (John Lithgow) decides to be like a father to Harry (French
  Stewart).  He hugs Harry, then ruffles his hair, at which point
  Harry's leg begins to twitch wildly (in an obvious reaction to the
  hair-ruffling).

----------------------------------------------------------------------------

The Boy With Green Hair (film, 1948) 
  Peter Fry (Dean Stockwell) lives with Gramp Fry (Pat O'Brien)
  as he is a war orphan.  In several scenes, adults are seen ruffling
  Peter's hair, which he appears to dislike.  Of course, hair is
  the touchstone (so to speak) of this film, as one morning Peter
  wakes up and his has turned green.  This serves as a device for
  the film's look at how people treat people who are perceived as
  different (green hair, war orphans, &c.).
    Click here for illustration.


----------------------------------------------------------------------------

Buffalo Bill (film, 1944) 
  Dawn Starlight (Linda Darnell) is a Native American schoolteacher in a
  Western town inhabited mostly by whites. One day, a shadowy figure comes
  into the schoolroom and gives her a private message. She announces that
  there will be no more school, as she must go back to "my people".
  She tells the children to go home and slowly walks down the aisle which
  separates the girls from the boys (as was the custom in many such frontier
  schoools). Looking at the children as if with fond memories, she pauses
  midway, and ruffles a boy's hair. (She never touches the girls, nor any
  other child.)

----------------------------------------------------------------------------

Dunston Checks In (film, 1996) 
  Kyle Grant (Eric Lloyd), son of the manager of the Majestic Hotel,
  meets an orangutan named Dunston (Sam) who has escaped from his
  cruel owner.  When Kyle and Dunston get to know and trust each
  other, Dunston ruffles Kyle's hair to signify that they have become
  friends with each other.  He does it again near the end, when it
  looks like they're going to have to part (but of course, they don't).
  Kyle's father, hotel manager Robert Grant (Jason Alexander) also 
  ruffles Kyle's hair as a sign of affection.

----------------------------------------------------------------------------

Mon Oncle Antoine (film, 1971) 
  In a small Quebec town, villagers are gathered in the local general store
  on the day before Christmas. A young woman asks the proprietress if she has
  a wedding veil, which tips everyone to the fact she is going to be married.
  The men immediately begin playfully taunting her boyfriend, a young man in his
  mid-20s, referring to him as a young stud and clearly congratulating him on
  his apparent sexual prowess. Several of the older men ruffle his hair,
  some repeatedly, in a gesture that seems to indicate that doing so puts them
  in contact with his virility or potency. 

----------------------------------------------------------------------------

Round the Twist (Australian Children's Television Foundation, 1989-2001) 

    "Skeleton on the Dunny", 4 April 1989
  NOTE: "Dunny" is Australian slang for an outhouse seat
  
  The kids have seen a ghost around the Dunny (outhouse), whose purpose
  in showing up was to let them know that a missing painting was hidden
  there.  After they rescue and clean up the painting, Bronson Twist
  (Rodney McLennan), 10, asks if the ghost will show up again, and Nell 
  (Bunney Brooke) says she doesn't think so, as she ruffles Bronson's hair.

----------------------------------------------------------------------------

The Simpsons (Fox, 1989-present, many episodes) 
  Homer and others ruffle Bart's spiky hair (often).

The Simpsons Movie (film, 2007) 
  Tom Hanks arrives in Springfield to promote the image of the EPA,
  which is ultimately planning to blow up Springfield, as it is too
  toxic.  After his glowing and heartwarming speech, a boy is so
  entranced that he gushes, "Tousle my hair, Mr Hanks" --- which he
  does.    
    Click here for illustration.

----------------------------------------------------------------------------

Tennessee Johnson (film, 1942) 
  U.S. Representative Thaddeus Stevens (Lionel Barrymore) calls on the new 
  president Andrew Johnson (Van Heflin) at the White House, just as Johnson 
  is telling his grandchildren Amy (Patsy Nash) and Andy (Dickie Hall)
  a story before bedtime.  As the childen say goodnight to Stevens,
  he ruffles Andy's hair and kisses Amy's hand, an obvious difference in
  response to boy and girl.

----------------------------------------------------------------------------

Two and a Half Men (CBS, 2003-2015) 

    "Apologies for the Frivolity", 23 October 2006
  Charlie Harper (Charlie Sheen) has to entertain his new girlfriend's children. 
  He knows nothing about them, as he has not yet met them. He asks his nephew,
  Jake Harper (Angus T. Jones) to participate, assuming that they'll get along 
  since they're all kids. Jake is not so sure. He warns Charlie that, if the 
  children are boys, he should not refer to them as "little dudes". Charlie 
  regards his advice as worthwhile, and asks, "What else ya got?" Jake makes 
  it clear: "No lame magic tricks, no head-rubbing, and please no high-fives. 
  And whatever you do, don't ask 'Who want's ice cream?' Everybody wants ice 
  cream. Even lactose-intolerant kids want ice cream!" Since Charlie is in 
  another room finishing this conversation with Jake, it is his brother, Alan 
  Harper (Jon Cryer) who answers the door. Alan did not hear the conversation 
  between Charlie and Jake. "Hey, little dudes, gimme five." is his opening 
  line. Charlie comes in to greet the kids, and before long the boys' mother 
  (Katherine LaNasa) makes them all uncomfortable, so Charlie leaves awkwardly. 
  Alan, trying to keep everyone happy, comes up with, "Hey, who wants ice 
  cream?" -- and rubs the oldest boy's head.    

----------------------------------------------------------------------------

The Zack Files (Fox, 2000-02) 

    "Pop", 24 February 2002
  Zack Greenburg (Robert Clark) lives with his father (Jeff Clarke). His 
  parents are divorced, and his mother (Gina Sorell) lives some distance away. 
  Zack is content living with his father, but he does miss his
  mother, and tells her so in eMails. His mother decides to 
  visit suddenly, and reveals her plans to move back to be closer to 
  Zack, which would put him in the awkward position of shuttling back  
  and forth between the parents several times a week. He decides 
  living with his father is what he wants, and figures out a way 
  to tell his mother at dinner in a restaurant, while still assuring 
  her of his love, and that he wants to see her occasionally. She 
  understands, and reaches across the table to smooth his hair in 
  a gesture of affection, but hesitates: "Oh, I guess maybe you're getting
  too old for me to mess with your hair." "I was too old years ago, Mom", 
  Zack says, "But you can still do it." She finishes the gesture, 
  in a touching scene (pun not intended).