There are some inherent qualities to homebrew settings:
1- a DM can design the world around the PCs
2- a DM can make the world evolve and change according to previous PCs actions without having concerned looks from his players (contrarily with an established settings - try to modify the FR with Thay who "won" a global war, you'll see some of your players getting worried).
3- you can take bits and pieces from great published materials and add them together to make a whole even greater than the sum of its parts.
4- most importantly, you can use whatever makes you thrill as a DM to build your homebrew. A thrilled DM will be better than a DM-not-so-thrilled. Almost always.
Now, speaking of my homebrew specifically, what makes it great is:
1- a combination of Arcana Evolved, Ghostwalk Campaign Option, Laelith (a French-developed medieval metropolis for D&D) and my own ideas which makes the whole better than the sum of its parts (see above).
2- player characters who are getting some influence in the world as they progress (they are now eighth level, and one of them will become a senator pretty soon, allowing for massive political plots with targeted adventuring/dungeon delving from time to time. That makes the characters part of the world, and the story about the characters in the world, not as outsiders.
3- have rule components that really emphasize the campaign I want to have. As the creator of the setting, I know more than anyone else what part of the setting is important for the campaign, so I'm able to represent these points in the rules. I can create specific Prestige Classes, specific character traits and rule variants to get the best out of the equation Game Rules + Campaign World.