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.
This article from The Charleston Mercury dated November 16, 1860 describes some of the flags which appeared early in the war.
I welcome your additions and corrections to this information.
The Citadel Battle Flag - "Big Red" was carried by the men of The Citadel when firing the war's first shots at the Federal ship Star of the West months before the attack on Ft. Sumter and remains her flag today.
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.