Doing PHP the *right* way

In this issue,
#2040739-4: Why the need for (php_)eval?

killua99 said:

Some people using it to run code, some people don't know how to make a module to make a preprocess or alter. So they use this php box to evaluate thing (not only HTML) and get the output they want.

I'm one of those people putting code into the PHP box, but I'd like to reform my ways! I mostly just use it for layout purposes: making two, or three column grids. Has anyone created a custom module that preprocesses or alters views fields before rendering the PDF? I've only scratched the surface of module development, but if someone can point me in the right direction it would be a huge help! Is there a particular hook I should use? A particular example module?

If I figure out how to do this, I'll post my solution here, but a little guidance could make this happen much faster :-)