There are many different ways to change the appearance of the stock Messages app on a jailbroken iOS device. The tweak Messages Customizer Pro adds a wide variety of options in one place to modify the look of message threads.
Besides pre-set themes to choose from, new themes can be created and completely customized using Messages Customizer Pro. Different themes can even be assigned to individual contacts or conversation threads. Bubbles for iMessage or SMS messages can also be independently customized.
Default themes to choose from include: Dark, Fade, Flat, Outlines, Translucent, and Translucent Dark. For those who would like to get a taste of Messages Customizer Pro, there is a free version with limited functionality as well.
Messages Customizer Pro is available from the BigBoss repo on Cydia for $1.50. Jailbreak iOS 7.1.x with Pangu to start customizing iOS. Check here for instructions on how to jailbreak iOS 7.0.x with evasi0n 7. You can also find out how to purchase and install Cydia tweaks with this guide.