I actually prefer them on the side in most cases. For whatever reason the aesthetic of top jacks always kinda irritates me except in select situations, like when the pedal is wider than it is tall, or on specially fabricated enclosures. Just depends, really. But it can be a deal breaker for me in many cases, vain as it is.
I only had side-jack pedals at first. Over time by chance I have now ended up with a greater total number of top-jack pedals. I find them easier to work with in general. I think it would be nice if either the industry would eventually just settle on one standard, or if companies like Digitech would make, say, the Obscura in both configurations.