I prefer sans-serif. I even prefer it for paper these days, there's still the occasional magazine that is set in sans-serif. Serif is pretty handy on low-quality paper though.
I force web-pages to be shown in sans-serif and I'd do the same to ebooks if they were locked to use a serif font.
There are books that use several fonts for effect though, like the Ruby Dynasty series by Catherine Asaro. The ebook-versions I have of those don't have the extra fonts so they become harder to read.
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