I repeat parts of their job description and explain why I fulfill it.

Example: Job ad says "we look for a proactive and self-reliant person" then my cover letter says "to successfully finish my PhD, being proactive and self-reliant was important". This technique works even better for the technical parts.

I'm not sure if it was worth the effort. In the german job market, employers are quite desperate these days. A friend sent out simple template letters and got interviews just as easily.

I always sent a PDF. If sent by email, I duplicated the cover letter in the email. My experience is that many had a print out at the interview and PDF works best to ensure a good print.