The Rune Lettered "P.L.E.A.S.E" at the end of Episode 3 of, where the Devices are requesting the potentially-dangerous Velkan Cartridge System to be installed. It just comes across as such a powerfully moving moment that the devices are taking dangerous measures that they know is the only way to help their wielders.
Most moments with Hayate and the Knights.
Fate and Alicia's goodbye when Fate is trapped within the book of darkness in her ideal world, as well as being a MAJOR Tear Jerker.
This exchange from episode 11:
Hayate: I'll give you a name. I won't let anyone call you the "Book of Darkness" or the "Cursed Tome". Those aren't you any more. *Reinforce starts to cry* I'm your administrator. I can do this.
Reinforce: It's impossible... The automated defense program does not stop. The mage from the Bureau is fighting, but that too is pointless.
Hayate: It's all right. [...] As Mistress of the Night Sky, I grant you a new name. One who supports and helps others. You are no longer cursed. You are a tailwind of fortune, a breeze full of blessings... Hello, Reinforce.
Part 17 of A's Sound Stage 3, where Fate tells Lindy, Chrono and Amy that her experience in the Book of Darkness enabled her to see herself as her own person, rather than a flawed copy of Alicia, and she accepts Lindy's offer to adopt her.
A's manga, chapter 6. When Nanoha suggests that a part of Reinforce still lives on as part of post-Unison Hayate, the latter bursts into tears despite her best efforts to stop. Nanoha and Fate's reaction? A (wordlessly!) synchronized double-sided Cooldown Hug.