Let's look at the last paragraph of Stardust, before getting into the epilogue:
He looked upon the lights of Wall for what he knew (it came to him then with certainty) was the last time. He stared at them for some time and said nothing, the fallen star by his side. And then he turned away, and together they began to walk toward the East. (10.220)
What does this tell us? Tristran found the fallen star that he set out for in the beginning of the book, and he's gotten to know her as a person and fallen in love with her. He's learned about his origins in Faerie (specifically his heritage as the grandson of the Lord of Stormhold), and he's wrapped up his business in Wall, like releasing Victoria from her oath to grant him his Heart's Desire and saying his goodbyes to his mortal family.
So now Tristran is off to explore Faerie and continue to have adventures, knowing his true identity, and with his true love by his side. Not bad, eh?
We get an additional wrap-up in the epilogue, though, which tells of Lady Una's homecoming to Stormhold. She holds down the fort while Tristran and Yvaine continue to travel, and when they eventually return, Tristran does a good job being ruler. There are allusions to the mysterious Fellowship of the Castle, which the airship captain and the hairy little fellow referenced earlier on, so we get the sense that Tristran has reconnected with his old buddies and is still fighting the good fight (a.k.a. against evil).
Eventually Tristran dies, which is a bummer, but Yvaine rules on, and does a decent job of things. Maybe this isn't the fairytale ending you were expecting, but it's more true to life, since, you know, people die. Tristran's left hand never recovers from the burn, which again, maybe you were thinking would be totally magically healed, but oh well. We make do with what we've got, and that seems to be one of the take-home messages in how Stardust ends: Do the best you can with what you've got, and hopefully a happily-enough-ever-after ending will come your way.