The most lethal earthquake in history is probably one that you never heard of--a May-July, 1201 earthquake that struck the eastern Mediterranean, including Egypt and Syria. It is estimated that more than 1.1 million people were killed. (See here). The earthquake is detailed in an article entitled "The historical earthquakes of Syria: an analysis of large and moderate earthquakes from 1365 B.C. to 1900 A.D." published in 2005 in the Annals of Geophysics vol. 48 (3) p. 347-435 (available at http://hdl.handle.net/2122/908).
As you may have gathered from my prior post that discussed the New Madrid Earthquake, really large earthquakes rarely are an isolated event, but that there are generally a series of earthquakes and aftershocks that may last weeks or months.
In the case of the 1201 earthquake, there apparently was a series of earthquakes between late May and extending into August. The primary quake--i.e., the most damaging--appears to have been on May 20, 1201, which destroyed Nablus, and heavily damaged Damascus and Tripoli. It also caused a destructive tsunami along the coast of Syria and on Cyprus. It was felt in as far separated places as northern Iran, Mesopotamia, and Sicily. This first earthquake apparently had little impact in Jerusalem and Egypt, though it seemingly caused the failure of the Nile floods.
There was a subsequent earthquake in June or July that caused destruction in Tyr, Beirut, Damascus, Baalbak, several towns in Palistine, Homs (in Syria) and caused a tsunami in Cyprus. A later earthquake in July-August collapsed monuments and temples in Baalbak (perhaps weakened previously?).
The article notes that many of the deaths may have been the result of the resulting famine, rather than directly as a result of the earthquake(s), which should be a further lesson for us on the importance of a good store of foodstuffs where feasible.
As for other quakes, this site has a list of the 12 worst earthquakes in history.