Sadly enough there aren't that many good Downton Abbey fics out there, at least no Thomas-centric ones.
But I found one that, on second sight, turned out great after all. And it's now my head-canon. Definitely.
So, here's one great Downton Abbey fic rec for you:
Alex51324 wrote "The Thomas Barrow Show" (link to AO3)
Summary: The Thomas Barrow Show follows the adventures of Thomas Barrow during series three of Downton Abbey. Find out what Thomas was up to during some of the times when the cameras inexplicably chose to follow those other people who are not Thomas, and what was going through his mind during the times that we did see him.
Why I think you should read it: 70391 words in eight chapters, each chapter a companion piece to the actual episode, with scenes and dialogue taken from the show mixed with other stuff. And although I had a bit of trouble getting into the story at first, on second reading it totally convinced me. This is what really happened. It's head-canon. And it's great. Especially the last chapter. The last episode is my favorite by far, and now with this background information and fillers... it's amazing.
The only thing I regret is that there isn't more. But I hope the author will go on writing the Thomas Barrow Show once Season 4 has aired.
Here's two excerpts that I like:
Thomas is talking to Mrs. Hughes:
“That’s what he said I was, something foul. And revolting. I don’t think I’m something foul. I know I’m supposed to, but I don’t.” He said it defiantly, but it was only half-true. He didn’t want to think so. He could tell himself that if, for instance, God was against it, God had no one but Himself to blame for making him that way. But he wasn’t quite so arrogant that he could believe, really be absolutely sure deep in his heart, that he was right about this, and everyone else was wrong.
And here's Thomas, trying to explain to Daisy 'the incident', you know, with Jimmy:
“I was caught-kissing somebody.”
Daisy gave him a skeptical look. “It must have been more than kissing if you got sacked for it.”
“What do you know about more than kissing?”
“Mrs. Patmore told me. When I got married. All about the facts of life.”
Thomas suspected she’d left a few things out. “It wasn’t more than kissing, as a matter of fact,” he answered. “It was more - who it was I kissed. And that the other person didn’t like it.”
Whisking egg whites with a serious expression, Daisy hazarded, “Lady Edith?”
“No!”
“Lady Mary?”
“No. It wasn’t a lady at all,” he hinted.
She set down the bowl. “Ethel?”
“Jimmy,” Thomas said, between clenched teeth.
“But-he’s a man,” Daisy said.
“I realize that.”
“What do you want to kiss another man for?”
“I just do.”
“But why? There’s no point to it, is there? You can’t marry or…anything.”
“Not marry, no. And if I go into any more detail, Mr. Carson will kill me.”
Go on, read it if you wanna know more about what Thomas did and thought in Season 3. You won't regret it.