Came here to mention Miguel. I think they handled it brilliantly. Letting him work right up til the end clearly meant a lot to him (iirc his dad, Jose Ferrer, did the same thing), and the denouement with his character's daughter meant a lot to *me*. That episode featured a song by the band he was in, the Jenerators, and even though I don't think he played in that particular song it made me tear up. The episode where his character left also featured a Jenerators song, this time with Miguel singing Knocking On Heaven's Door.

I wasn't a big NCIS: LA fan, but I was a big Miguel fan, and the people working the show very obviously loved him a lot. That alone meant a lot to me.