If you're looking for a GUI, the Okular document viewer (by KDE) can sign them just fine, as can LibreOffice (but I don't like how it handles key storage on Linux). For something much more powerful (where you can tweak every possible signature parameter), take a look at jsignpdf - the UI isn't exactly friendly, but it works more reliably than anything else and I've never seen a reader that didn't accept its signature (Adobe Reader likes to sometimes ignore signatures from other tools for no good reason, but never jsignpdf).

As for libraries, you can use jsignpdf from the CLI, PyHanko for Python and probably even more that I don't know.