MindBending Software produces nifty products that inserts subliminal messages into games. This is accomplished by intercepting GL calls and layering new graphics on top of it. They also can perform some trippy transformations to get your zen on. Unfortunately, it’s really expensive, most modules will run you between $700 and $1100. Ouch.
In particular, take a look at some of the videos they have online. I dunno if putting images of Jesus in a kids game of Grand Theft Auto is really going to help them. Interesting technology none the less.