"Holy crap on a cracker!" is something that someone might say when surprised or shocked.
The only place I have heard this phrase is on a popular show called, "The Big Bang Theory". One of the main characters, Penny, said this when she saw one of her friends kissing somebody.
"Holy crap!" is something one might say in surprise.
The "on a cracker" part is more difficult to explain: One of the jokes on the show is that Penny is from the Midwestern United States, where people have a distinct accent and manner of speaking. People from the Midwest have a lot of colloquialisms that other people in the US find amusing or funny. I'm not sure if this phrase is a Midwestern colloquialism, but it sure sounds like it could be one.
It's also possible that this phrase just sounds funny because it has rhythm and repeated sounds. Plus, the literal image of holy crap on a cracker is funny, too!