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I believe that if you pay close attention, you'll see that there are many parallels regarding scenes, songs and quotes which are too numerous or meaningful to just be coincedental.
When Bonnie and Elena are in the car, and Bonnie is telling Elena she's psychic, Elena challenges her to "Predict something about me."
Bonnie: "I see..."
(A crow hits the windshield.)
Bonnie: When I touched you, I saw a crow.
Bonnie: A crow. There was fog...and a man.
Damon is always saving Elena -
He picked her up and carried her away from the crash in 1x11.
He picked her up and carried her to Stefan in 2x21, and into the witch house.
He picked her up and carried her out of the hospital in 3x05.
Scenes featuring him returning her necklace and/or putting her necklace on:
1x14, 2x08, 3x01 and 3x05.
Scenes featuring Damon in Elena's room or where they are in bed together:
2x22, the deathbed confession.
3x03, Elena wakes up and finds Damon lying in her bed and freaks out.
3x08, Elena finds Damon lying on her bed and instead of asking him to move, gets into bed beside him and turns her bedside light off.
3x19, In the motel room, Damon notices that Elena is awake and lies down on the bed next to her.
Scenes featuring handclasps:
1x19, at the Miss Mystic Falls pageant
2x01, in Elena's bedroom
2x10, in the cave
2x18, at the decade dance
2x20, in Damon's bedroom
2x22, on Damon's bed
3x06, in the training room
3x19, in the motel room
In 2x01, Katherine says hate is the beginning of a love story, and the episode ends with Elena saying "I hate him" to Stefan. Song lyrics heard at the opening of the scene when she walks into her room and finds Damon there:
"I get lost in the beauty of everything I see
The world aint half as bad as they paint it to be
If all the sons, all the daughters
Stopped to take it in,
Well then hopefully the hate subsides
And the love can begin, it might start now
Maybe I'm just dreaming out loud."
Song heard when Damon tells Elena he doesn't deserve her "But my brother does", 'I Was Wrong'.
(Damon also says this in 3x02 in Elena's bedroom).
When Damon tells Andie in 2x13 "I'm in love with a woman I can never have", the song heard in the background is 'Losing Your Memory', a reference to 2x08 when he compells Elena to forget his confession of love perhaps?
There are frequent DE quotes about "not leaving" each other:
Damon: I can't lose you. (2x20)
Elena: I'm here until the very end, I'm not leaving you. (2x22)
Damon: I promise you I will never leave you again
Elena: I am not going to leave you. (3x18)
Song titles to every scene DE have kissed -
2x01 'Come Home' ('Come home, come home, cause I've been waiting for you for so long, so long'.)
2x22 'I Should Go' ('I should go before I lose my sense of reason/And this hour holds more meaning than it ever could/I should go, I should go')
3x10 'Holding On and Letting Go' ('It's one door swinging open and one door swinging closed/Some prayers find an answer, some prayers never know/We're holding on and letting go.')
3x19 'NEVER Let Me Go'
Caroline: Damon's gotten under your skin. (3x04)
Elena: He got under my skin and no matter what I do, I just can't shake him.
Matt: Once you fall in love with someone I don't think you can ever shake them. (3x16)
I know this list of parallels is open to interpretation and people can argue that they don't have to mean anything, but in this show, it usually does. These are just some of the parallels from Seasons 1 to 3. There are many more: link
I don't want to over-exaggerate anything, because there are Stelena shippers who look at Elena saying "It will always be Stefan" or even Klaus' "That kind of love never dies" and use those quotes as hard evidence for Stelena being the prime couple of the show or as an argument for endgame. Then again, why have the writers put in all these parallels for Delena, but not Stelena? If Stelena had all these parallels, then wouldn't their fans use them as an argument for why SE should be endgame? Of course they would. The parallels DE have had don't need to be there, but they are, and they can't be for nothing.