The packaging of these cartridges has changed when Canon came out with printers using 6 ink cartridges of these BCI, this change was so that there wouldn't be too many different lines of ink cartridges.
The one difference is the composition of the black ink. The BCI-3e Black is a pigment based black ink. while the BCI-6 Black is a dye based black ink.
Pigment based ink is intended for crisp black and white text, while the dye based is for better photo quality.
The E stands for ENHANCED compared to the older BCI-3.