First you will shown the different email accounts set up on your iPad or iPhone mail app, you can select the different colors for each email account.
Then you can select the configure button on the upper right and select how the color will be indicated on each different email account.
I have selected shaded background as shown below, this is one of the more useful configurations as the entire email shown on the left sidebar is colored for the different email accounts on your iPad.
Color Mail Labels is available for jailbroken iPads or iPhones and can be downloaded from the Cydia store for $0.99. How many email accounts do you have?