North on the server is the direction that the sun, moon and clouds move towards.
For a long time there was never a general concensus on north - an issue complicated by Notch's completely arbitrary axes. However, most people chose to assume the sun would follow a natural path (for Earth), IE rising in the east and setting in the west, which led to the most common assumption of north. This also meant that clouds travelled north (an anomoly, as this does not generally happen in the real world, but more weight was given to the sun than the clouds).
When v1.0 was released, Notch said we had it all wrong, and had changed the sun and moon direction in the code. This screwed up many, many things - instantly all maps were wrong, directions were wrong, houses and areas set up to specifically take advantage of sunrise and sunset lost their views and naming conventions went out of the window.
There was no quick or simple solution (rotating the map is simply not feasible), and amidst much languishing, the decision was taken to simply continue with our previous notation, as this did not destroy our extension road and hub networks. The sun rising and setting in the wrong direction is lamentable, and we still hope for a solution, but for now simply has to be endured for the greater good.
As of the update to version 1.7.2 of Minecraft with the introduction of sunflowers, because of this issue it should be assumed that the sunflowers always face south.