EQG 1:
1.1 First time meeting Pinkie Pie in CHS - Pinkie asks if Twilight has a twin sister living in the city and has a pet dog named 'Spike'. Reference to EQG 3 it seems.

EQG 2:
2.1 The blast of Equestrian magic - Remember before the 6 defeated Sunset? Well, it seems that this part happened during that.
2.2 The sleepover - The game cover is a reference to that MLP episode, a parody of Marvel's comics.
2.3 Practicing in the barn - Rarity goes Daft Punk.
2.4 The very end - This kind of shows what EQG 3 is going to be like, so this could be considered a little hint.

EQG 3:
1.1 Birthday of who's? - After the intro, you can see that there's a birthday present on the 30th day on the calendar. Not sure what month but as Twilight was pretty much lonely at the time, I can only assume it's hers.
1.2 Information gathering - Before Twilight enters her room, the board is displayed showing things such as pictures of the Equestrian magic rainbow (links to EQG 1/2) and the broken red gem (clearly left on the stage, EQG 2).
1.3 Twilight's first song - It's very similar to EQG 1, especially the window being covered.
1.4 Evil Twilight's portals - A Pegasus on the other side of the portal saw the portal open and is surprised in portal 2. Pony in portal 3 was already running away. Portal 7 shows a pony noticing the portal being opened and also being surprised.
1.5 Where have you been? - In the very last scene, the Twilight from Equestria finally arrived with the reason of being "trapped in a time travel loop". Could this shown in a future MLP episode or maybe in a future movie? Who knows? EDIT: After a quick read-about, it was said to be part of the season 5 finale.