There are probably some Strange New World stories that focus on the dim and distant future and probably a shed load of fan fiction, the thing though about fan fiction is that it's kinda irrelevant around here as the authors may read them and take ideas from them so they can't be discussed here. Of course, you can always go down a few levels and ask in the fan fiction section.
I believe the story "Guardians" by Brett Hudgins, in Star Trek: Strange New Worlds VII, takes a loooong view of Trek history. ;-) It was the second place winner in that volume. My story "The Law of Averages", which is in that same volume, centers around Dax about 700 or 800 years after the events of DS9, and it mentions several changes that have taken place in the intervening centuries. I'm not aware of any novels, though.
Not sure how you define far future, but my Department of Temporal Investigations: Watching the Clock offers some indirect glimpses into future centuries as far ahead as the 31st. Crossroad by Barbara Hambly gives us a glimpse of the 26th century or thereabouts, or at least one possible version thereof.
Not for long(but a paragraph from memory), but Federation gives us a glimpse of about as far forward as I think I've seen in any trek book. It's also one of the best trek books there is.
Oh, wow. Amy Sisson another published author!. This is to Christopher and Amy or any other Author, have you guys heard of http://www.reddit.com/ ?. There's a section called "IAmA" here http://www.reddit.com/r/IAmA/ where you state who you are and people ask you questions. Its a great way to promote upcoming books and connect to some readers. Various peoples have done it even famous ones (Stephen Colbert, Roger Ebert) I've even seen one done by John Scalzi. If it sounds interesting please do one. I'd be very interested in it
Robert Jeschonek's "Our Million Year Mission," from Strange New Worlds VI (I think it's 6, that is) is further out chronologically. That it is.
How far into the future was the last chapter/paragraph of Federation? (think I'm thinking of the right book...) That was way way out there.
All that was said time-wise was "a thousand years distant" in Kirk's description, which might've been wrong. Still, even if he was wrong, the tech didn't seem near as far along as either of the SNW stories that were referenced earlier in the thread. If you're talking about Trek fiction outside SNW though, I think that would be, yes.