> Some link viruses got popular. […] My main Amiga setup
> also got infected quite badly once...

In recent years, I had my MorphOS system infected with an Amiga link virus. Of course, it did affect only m68k binaries. I only noticed it years after the initial infection happened (retraceable by looking at the file dates) when I was comparing the installed ReAction classes with those on my OS3.9 CD. I noticed that the files on the HD were bigger than those on the CD. Viewing the bigger files in hex mode revealed the infection. VirusZ then found all the m68k binaries that got executed or accessed during those years to be infected. I could retrace the infection to a time when I used to test loads of m68k software from Aminet for MorphOS compatibility (so nothing to do with piracy should anyone suspect this).
Unfortunately, I forgot which link virus it was, but I remember it was a well-known one (it may indeed have been one of the HNY variants).