Please temper my answer with a grain of salt since I don't play a tank... but I do play a warden so I have to keep them standing!
At any rate, guardians are the mainstay of the tanking archtype. They have the best taunts and so can maintain aggro when no one else can. They also have the largest health pool so they tend to be able to take the most damage.
Zerkers are kind of like a hybrid plate-tank being part tank and part DPS. Their damage output is higher but they can't MT or single tank as many of the end-game high-end instances as a guardian can.
For a while, I was raiding courts in T6 and we used to keep both a guard and a zerker along with 3 healers (mystic, warden & temp) in the MT group. The two of them would switch off MT depending on which name we were on.
Since I regularly group with both and as MH in the MT group on a lot of my guild's raids, I can tell you that from my point of view when well played there is little difference between them but my money still goes on the guardian every time!