Love at first sight on 1x04 "Raising Hell"
From the moment Magnus and Alec met sparks were flying. You can tell from Alec's nervous smile and the way he can't keep his eyes off Magnus that he is crushing hard.
Magnus and Alec get back together on 2x20 "Beside Still Water"
When Magnus and Alec are together it almost feels like everything in the show is going to be okay. When they were apart the world was very literally falling apart around them. Alec tells Magnus that he can't live without him, and we connected with Alec on a spiritual level.
A magical dinner by the fire on 2x17 "A Dark Reflection"
When Alec misses their date, Magnus brings the date to him with a wave of his hand. Having a boyfriend with magic powers sure does come in handy.
Alec (literally) gives Magnus his strength on 1x06 "Of Men and Angels"
Even warlocks can run out of power and Magnus was fading fast. Thankfully, Alec was there to offer his own strength in whatever way he needed. Magnus was obviously surprised by Alec's inclination to help him and admitted that it's rare to find a Shadowhunter with such an open heart.
The aftermath of Valentine's destruction on 2x12 "You Are Not Your Own"
This entire episode was absolutely tragic. When Magnus is hurting so is Alec, and the devastation when he realized he couldn't take away Magnus' pain is agonizing. This moment may not be a happy one, but it definitely made us emotional.
Alec opens Magnus up to love for the first time in a century on 1x06 "Of Men and Angels"
Although Magnus had been in love with both men and women before, he closed himself off from feeling anything for anyone for almost a century. But from the moment he met Alec his heart immediately opened back up. If that's not true love than what is?