While it doesn't seem like much at the time due to Thomas also giving selfish reasons to help Harry through the first few books, it all takes another meaning when you (and Harry) find out that Thomas is Harry's half-brother and has been subtly looking after him.The Reveal via soulgaze was heartbreaking in the good way.
Hell, Thomas has just retroactively proved Harry's 'familial dementia' theory. And it is beautiful.
After Harry and Thomas share the soulgaze where they both get to see their mother, Harry has a brief but powerful moment:
The aching, lonely old hurt was overflowing me. But I suddenly found myself laughing. I had seen my mother with my Sight. I had seen her smile, heard her voice, and it was something I could never lose. Something no one could ever take away from me. It couldn't wholly make up for a lifetime of loneliness and silent grief, but it was more than I ever thought I would have.
After Harry kicks Ebeneezer out for being a Blackstaff he's sitting in his apartment, feeling alone and sorry for himself. Then the puppy he saved comes up and starts licking him, and Mister starts rubbing up against him too, almost as if to comfort him. Then, Mister starts batting at the puppy and Harry laughs. Maybe I'm a sap, but it really made this troper tear up a little bit and get all warm and fuzzy.
I laughed. I couldn't help it. The world might be vicious and treacherous and deadly, but it couldn't kill laughter. Laughter, like love, has power to survive the worst things life has to offer. And to do it with style.
Practically every scene with puppy Mouse qualifies, for that matter.
Thomas using up all but the last dregs of his savings to pay off Kincaid for Harry.