I tried Calibre, but found it absolutely horrible. It insist on 'managing' a library of ebooks, whereas I just need a simple PDB → EPUB converter, nothing else. Seems I have to import directories and keep all kinds of accounts and profiles and whatnot. Why 'import' at all (and what happens if I move or delete the ebook later on), I don't need all that. Way too overcomplicated for what I want: simply convert an ebook and be done with it.
However, I found two alternatives that may come in handy:
1.
http://www.2epub.com/ seems to do pretty decent job (if Kobo could do the same internally for reflowing PDFs, that would be great!)
2.
http://willus.com/k2pdfopt/ changes the layout of PDFs to fit on an ereader. A rather arcane interface, but kinda works OK.
Still find it ridiculous I have to do all this crap manually to properly read PDFs (if some random free piece of software can do it, why couldn't Kobo just build in something similar) but at least I can use my ereader for the purposes I intended.