I've been quite happy going from HTML to ePub (using Calibre). I generally don't use the GUI, though; I've been using html2epub on the command line. I'm sure that Calbre uses that under the hood, since it's all by Kovid anyway.
The forums have a lot of good tips for PDF conversion... but I've had mixed results. I read a lot of academic papers, and some convert better than others. I've largely given up, and just drop the PDFs on the reader; for me it's easier to squint with the occasional small type than spend too much time messing around with different converter applications.
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