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I'm afraid there's no "magic bullet" that will fix all known epubs. It depends on the HTML/CSS that was in the source file you converted to epub. Having said that I don't believe there is a single epub which cannot be fixed by appropriate tweaking.
The first place I'd be looking is in the epub's internal css file. Look for occurrences of font-family:"some font name" where "some font name" is the "wrong" font name. Try tweaking to the "right" font name as specified in your Calibre extra CSS.
If you're unlucky the problem may be that every single paragraph in your book's source file contained a style='font-family:"some font name";' statement with the "wrong" font name. I've often seen this when the original source is a LIT or RTF file. This is more of a pain to fix but perhaps can be done by modifying your usual Calibre extra css @font-face statements when doing the initial conversion.
If you need more help with a specific book and there are copyright issues with posting here, you could send me a PM and we can find a way for me to see your source file.
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