LibreOffice's apps and Inkscape also do the job as they say, but they re-render the existing content which often changes it's look. In particular of it don't have a close matching font installed the result can be a mess. xournal doesn't have that problem but it only lets you add, not delete or modify.

No mention of digital (x509) signing. LibreOffice can do it - but see above. Okula can do it reasonably well, if you are prepared to pollute your Firefox certs with your personal ones. I haven't found a command line tool (like pdftk) that does it, which is sad.