Grave Marking Scene

An expression of Pet the Dog, this is where a character is shown visiting the grave or site of death of a loved one as a periodic ritual. Often a Tear Jerker.

Examples of Grave Marking Scene include:

Anime

Maison Ikkoku uses the yearly visits to Soichiro's grave as a convenient way to say "another year has passed."
Darker than Black has this with April and July following November 11's death. Belying the fact that Contractors and Dolls are supposedly emotionless, they mark his site of death with beer bottles.
In Rurouni Kenshin, Kenshin and Kaoru visit the grave of his first wife and are surprised to find the grave already cleaned and her momento left there.
While its not shown if this occurs regularly, both anime versions of Fullmetal Alchemist show Roy Mustang leaving flowers at Hughes' grave on at least one occasion after his death.
Neon Genesis Evangelion plays this stright and inverts this, with both Gendo and Shinji Ikari visiting Yui's Grave. Marking the day she was absorbed into Unit 01. Even Gendo points out that 'This is just a marker.' You could say that Shinji is doing this every time he pilots.
Gunslinger Girl. Jerkass handler Jean is shown visiting the grave of his Dead Little Sister who was killed by terrorists, sparking off his Roaring Rampage of Revenge.
In Monster, one of the epilogue scenes is of Lunge leaving a bottle of liquor at Grimmer's grave, in reference to the promise they'd made to share a drink after everything was over.

Comic Books

Spider-Man often shows Peter Parker visiting Uncle Ben's grave.
Empowered visits the grave of her daddy, whom she lost early in her life.

Film

In the 1989 Tim Burton Batman film, Bruce Wayne regularly deposits a pair of roses at the site of his parents' murder.
For Your Eyes Only opens with James Bond visiting the grave of his deceased wife.
In Rocky Balboa, Rocky is shown regularly visiting and "talking" to his dead wife at her grave.
In Grosse Pointe Blank, Martin at one point visits the grave of his father, pouring a bottle of whiskey on top of it with a stone-faced expression, before dumping the bottle by the gravestone and wandering off. It's less about respect, and more about the implication that his dad was an abusive drunk.
Virginia in Happy Birthday to Me visits her mother's grave periodically.
In 2004 version of Phantom of the Opera, Raoul visits Christine's grave at end of the film. When he gets there, he notices that Eric has been there too.
Lionel attempts to visit his mother's grave after she is buried in Braindead. Ass-kicking for the lord ensues.
Connor and Murphy MacManus visit the grave of their friend and partner, Rocco, in All Saints Day, only to discover that the photo on his grave is his embarassing mugshot, complete with a whited-out police arm holding his hair out of his face. Hilarity Ensues.
Major plot point in The Crossing Guard is Freddy finally visiting his daughter's grave and accepting that she is gone.
Near the end of Forrest Gump, Forrest breaks down at the graveside of Jenny.
Martin Riggs is shown visiting his deceased wife's grave periodically throughout the Lethal Weapon series.
In Hyakujuu Sentai Gaoranger VS Super Sentai, Yuusuke/Red Falcon is seen visiting the graves of his former friends (don't worry, they were on the enemy side; his teammates are still alive).

Literature

Discworld has an example featuring an actual dog, where Lord Vetinari places bones on the grave of his beloved dog, Wuffles.
Truth in Television: Edgar Allan Poe.
In the last book of The Emigrants series Karl Oskar regularly visits Kristina's grave.

Live Action TV

Parodied in The Goon Show episode "Dishonoured" (remade as "Dishonoured Again"):

How that battle raged - I saw the whole thing on television, you know. Seagoon fought like a madman - how else? But alas... On that spot is now a little white stone. Once a year Min lays flowers on it. The stone bears a simple inscription in Hindustani. I haven't the heart to tell her that roughly translated it says "Bombay 49 Miles". Goodnight.

A Jack Bauer Fact states, "Every year, Jack Bauer lays flowers on Teri's grave, and then empties a full clip of bullets into Nina's."
Sun and Hurley visit Jin's grave on Lost as a way of letting the audience know he's dead. Except of course that He's Just Hiding!
Parodied in Mongrels. A guide dog explains to Destiny that since his owner can't see, he is free to lead him anywhere he likes. Cue the owner placing a bouqet of flowers next to a trashcan and saying "Hello Mother".
Bones does this often, and sometimes runs into her father, or at least finds that her father visited recently.

Theater

The widows' visits to their dead husbands' graves are a regular element of The Cemetary Club. (And the chance meeting with a widower visiting his dead wife's grave sets off the plot.)

Video Games

Parodied in Postal 2, where one of the protagonist's errands is to visit his father's grave...and pee on it.
In In Famous Cole visits the grave of his deceased girlfriend. When he has nowhere else to go, he sleeps beside it.
In Chrono Trigger you can visit Toma's grave in 1000 AD, and then go talk to him in 600 AD. He gives you his favorite booze to pour on his headstone.
In Red Dead Redemption, Jack does this at the grave of his father John Marston who had been killed by Ross 3 years earlier and his mother who had died recently of disease in depressingly sad rain to set the mood.

Western Animation

In the Batman: The Animated Series, Bruce Wayne visits the place where his parents were killed once a year, on the anniversary of their death, even as a very old man in Batman Beyond.
Parodied in SpongeBob SquarePants where Mr. Krabs witnesses Squidward sadly leaving flowers at a grave. After he leaves, Mr. Krabs walks up to tombstone and reads off it. It says "Here Lies Squidward's Hopes and Dreams."
- ..."What a baby."
- At the end of "SpongeBob Versus the Patty Gadget", SpongeBob collapses after the fight and we're shown a close-up of the spatula dropping from his hand. It immediately cuts to Squidward placing flowers on the grave, which SpongeBob then dances on, celebrating the titular Gadget's demise.
In Avatar: The Last Airbender, Iroh sets up a shrine for his dead son, and then starts crying. One of the saddest scenes in the series.