For most people, the image of the Confederate Flag conjures up the "blue cross with white stars on a red background" which is more properly known as the Confederate battle flag, but in fact, there were a number of Confederate Flags used during the war, and many regiments and companies had their own unique flags.
A discussion of flag construction techniques
This article from The Charleston Mercury dated November 16, 1860 describes some of the flags which appeared early in the war.
While I am by no means an expert on the various flags, I have tried to list below the ones of which I am aware. I welcome your additions and corrections to this information.
The Bonnie Blue Flag - The unofficial first flag of the Confederacy. Though never adopted by the C.S.A., this flag was "first" in the hearts of the people.
The Palmetto Guard Flag - The first southern flag to fly over Fort Sumter
The South Carolina Secession Flag - The symbol of secession.
The C.S.A. Navy Jack - This flag was used as a navy jack at sea from 1863 onward.
The First National C.S.A. Flag - The Stars and Bars was used as the official flag of the Confederacy from March 1861 to May of 1863.
The Second National C.S.A. Flag - The Stainless Banner
The Third National C.S.A. Flag - Officially adopted but very few issued.
The Confederate Battle Flag - The symbol of the South
Robert E. Lee's Headquarters Flag - Uniquely used to identify Gen. Lee's Command Center