Here's the second part (Seasons 7 to 12). The first part (Seasons 1 to 6) are in a separate post.
Season 7
[2F20] Who Shot Mr. Burns? (Part Two) ... when he is arrested for the attempted murder of Mr Burns ... Wiggum, directly after this, says: "Yeah, that's what they all say. They all say 'D'oh'." ... when he drops one of his two ice creams while driving ... when Mr Burns still cannot remember his name
[3F03] Lisa the Vegetarian ... when he invites Ned to a barbeque after saying that he wouldn't
[3F04] Treehouse of Horror VI ... when he finds out that the colossal donut is actually a small one
[3F05] King Size Homer ... as a bucket of bolts misses him while he is trying to injure himself: "Must hurt self... must hurt self..." ... when Lenny tells him that each push up includes both an up part and a down part ... after saying "fat, don't fail me now!" his tires burst as he sits in the car
[3F06] Mother Simpson ... Mother Simpson, when she bangs her head on her van.
[3F08] Sideshow Bob's Last Gleaming ... when he backs the car over tire spikes in a parking lot
[3F09] Two Bad Neighbors ... when he says something clever and no one was around to hear it ... upon discovering that George Bush is ahead of him at the drive-thru ... when he fails to get the last word in an exchange with Bush. ... Homer & Gerald Ford, when they both trip over.
[3F10] Team Homer ... Otto, when he chokes while bowling ... Homer, Otto, & Apu, during their team spirit song: "Go Moe, go Moe, don't make Homer shout out D'oh!" ... Moe, after he hits Burns' kneecap back in when he is trying to cripple him
[3F14] Homer the Smithers ... when Burns throws a book at him ... when Smithers hits him over the head with the phone [four times]
[3F17] Bart on the Road ... when he is asked an awkward 'Truth' question in 'Truth Or Dare?'
[3F18] 22 Short Films About Springfield ... when Maggie gets trapped in a newspaper vending machine
[3F22] Summer of 4 Ft. 2 ... when the fuse on his already lit firework burns off.
Season 8
[4F02] Treehouse of Horror VII ... when an alien whips him ... when he accidentally shoots Bill Clinton and Bob Dole into space
[3F23] You Only Move Twice ... when Hank Scorpio answers the telephone instead of catchng Homer as he falls backwards
[4F03] The Homer They Fall ... when Marge tells him he must see a doctor... a competent doctor ... when Drederick Tatum hits him in the head ... when his head hits a beam right after Moe tells him he's safe
[4F05] Burns, Baby Burns ... when he tries to hide in an abandoned warehouse which is full of activity
[3F24] El Viaje Misterioso de Nuestro Jomer (The Mysterious Voyage of Homer) ... when, trying to cool down his tongue with ice cream, it melts before it can reach his mouth ... while waiting for a very slow tortoise to write a message ... when he wakes up is a sand bunker and is hit by a golf ball
[3G01] The Springfield Files ... when he is told that the "Homer Is A Dope" T-shirts sold out in twenty minutes
[4F10] Mountain of Madness ... when a second avalanche traps him and Mr Burns just as they escape from the first one
[4F12] The Itchy & Scratchy & Poochie Show ... after his brain tells him: "Now look sad and say 'D'oh.'"
[4F19] Homer's Enemy ... Frank 'Grimey' Grimes, when imitating Homer [three times]
Season 9
[4F22] The City of New York vs. Homer Simpson ... when he discovers his car is being ticketed again as he is in the bathroom ... when he get a car boot stuck on his foot
[3G02] Lisa's Sax ... when Lisa informs him that he was supposed to tell her the story of how she got her saxophone. ... after dropping the saxophone on his foot while asking for an inscription ... Lisa, reading the inscription on her new saxophone: "Dear Lisa: May Your New Saxophone Bring You Years Of D'oh!"
[5F02] Treehouse of Horror VIII ... when the mutants start to attack him after he has teased them
[5F01] The Cartridge Family ... after realizing that he didn't rob the Kwik-E-Mart: "Oh well, I'll rob it next time."
[5F03] Bart Star ... when Bart throws something at him
[5F11] Das Bus ... upon learning that the company name 'Flancrest Enterprises' is already taken
[5F12] Dumbbell Indemnity ... when he realizes that he shouldn't have stopped Snake stealing Moe's car ... when he misses the opportunity to have the 10:15 train smash into Moe's car
[3G04] Simpson Tide ... when he realizes he shot the Captain out of the torpedo tube ... after the path of the submarine collides with the directional compass marker on the map
[5F14] The Trouble With Trillions ... when he realizes that he has to pay taxes every year
[5F09] Trash of the Titans ... when he has to take the trash out ... after Quimby tells him that the garbage men won't work for free
[5F16] King of the Hill ... when a paperboy hits him in the head with a stack of newspapers while he is jogging (twice) ... when he hits his head on a rock, sliding down the mountain ... when he realizes he still has four vertical miles to go on his mountain climb ... discovering that he left his wallet on top of the mountain
[5F17] Lost Our Lisa ... when he hits his head on a traffic light riding the cherry picker ... when his head gets caught between the two sides of a draw bridge
[5F18] Natural Born Kissers ... after a storage compartment opens and hits him on the head ... when everyone takes a picture of him and Mage naked (after he sarcastically tells them to)
Season 10
[5F22] Bart, the Mother ... as he is repeatedly hit by balls in a batting cage [many times] ... when he falls down the stairs to the basement because there is not light bulb
[AABF02] D'oh-in' in the Wind ... after Wiggum shoots him, embedding a flower in his forehead
[AABF07] Wild Barts Can't Be Broken ... after hearing that more of his secrets will be revealed on the kids' radio program ... when it is revealed that he has been practicing medicine without a license
[AABF09] Homer to the Max ... when he walks into a cactus [twice]
[AABF12] Make Room for Lisa ... when Bart trades his 'special Saturday' for a dessert
[AABF15] Mom and Pop Art ... when he throws his own doormat out of the window of his car ... when he is drenched in his dream by the 'dripping clock' painting
[AABF17] Monty Can't Buy Me Love ... when he closely misses out on winning the jackpot at the Vegas Town Casino
[AABF18] They Saved Lisa's Brain ... when Dr Steven Hawking hits Homer with a springing boxer's glove
[AABF20] Thirty Minutes Over Tokyo ... when he drops his watermelon which has changed its shape from a square back to the original round shape ... when the family's last million yen gets blown away in the wind [in Japanese] ... as he is being beaten with sticks by his blindfolded family [twice] ... Barney, dressed as Homer, trying to put beers on his tab: "D'oh! Woohoo! Uh... that boy ain't right!"
Season 11
[ AABF19] E-I-E-I-(ANNOYED GRUNT) ... when he picks up gummy bears to plant by accident ... upon remembering why the family left town in the first place
[AABF21] Guess Who's Coming To Criticize Dinner? ... when he realizes he has taken the kids to the zoo, instead of the Springfield Shopper [echoed]
[BABF01] Treehouse of Horror X ... when he runs out of gas ... when the freezer hits him with ice cubes
[BABF05] Take My Wife, Sleaze ... upon realizing that the biker gang have taken Marge
[BABF11] Missionary: Impossible ... when Bart goes outside to play on the swing, instead of helping him ... when PBS traces his call to pledge $10,000 ... when, in a game of roulette, the crab moves from the number he chose (6) to 31
[BABF12] Pygmoelian ... when Moe tells him that he was going to sell the bar to Hooters, but changed his mind
[BABF19] Behind The Laughter ... after passing a sign saying "Hollywood - 500 miles," after having previously passed one saying "Hollywood - 90 miles" ... when a lobster bites him on the nose
Season 12
[BABF20] A Tale of Two Springfields ... when Bart tells him the arena that The Who are playing in is in Olde Springfield, not New Springfield ... Bart, when Homer, instead of using his bottle of chloroform on the guard, tries to trade it with him
[BABF17] Insane Clown Poppy ... when, looking for a violin, he open a violin case which actually has a gun in it ... Krusty, for the same reason, just after Homer
[CABF04] Homer Vs. Dignity ... when a cyclist rides over him
[CABF03] The Great Money Caper ... when he enters the gift shop addition, after thinking he had left ... Bart, when his 'old man' disguise is infiltrated and he is arrested
[BABF22] HOM? ... when a rat has quicker reactions than him [twice]
[CABF11] Bye Bye Nerdie ... the 'Baby Safety' woman, pretending to be a baby, trying to get the lid off a bottle of baby powder.
[Seasons 1 to 6 in a separate post!]