Short answer is there is no real difference.
You will have the same services available on both sides. There are banks, NPC's with quests, merchants, crafters, everything.
Freeport is a darker and more evil place, while Qeynos is a brighter and cheerful place.
There may be an issue with spell availability. In Qeynos (and associated zones) there may be more loot drops for "good" classes, and in Freeport (and associated zones) there may be more loot drops for evil classes.
So if you're an evil class in Qeynos, buying from the broker, there may not be as big a selection. There is a fence where folks can sell between the two sides, but the markup is huge.
Anyone know otherwise?