My main recommendation is to prepare your resume in multiple formats. I'd also recommend that one of the formats be plain text, and that you should use plain text for electronic submission.
Almost by definition, everybody can read HTML. PDF is a good choice too, as many readers are freely available, and it preserves formatting well. However, once you submit a resume you have no control over how it is processed. It might be printed out or faxed and then scanned and OCR'd. Somebody might decide to scrape the text out of whatever format you provide, or cut and paste just the text. I've received emails with horribly mangled text that was somehow derived from the nicely formatted document the candidate had submitted. For electronic submission, plain text is the least likely to be mangled in transit.
If you prefer something like HTML, MS Word, or PDF, use as little formatting as possible. It's quite likely that the fancy fonts, boldface, and italics you've chosen won't survive by the time the document reaches the eventual reader. Use simple headings and use lots of whitespace to separate headings and paragraphs. Also, avoid multiple columns or inset text. If any text is cut-and-pasted, it might interleave text from the different columns when it's pasted. This will leave the result all but unintelligible. Worse, most people along the chain from you to the eventual reader won't notice and probably don't care that much about the fidelity of what they pass along.
As someone who reads resumes and interviews candidates, I'm aware of all the formatting pitfalls and try to look past these issues. However, I suspect others are much less forgiving, and so malformatting will reflect badly on you. If formatting is bad enough, it'll make your resume too hard to read, and they'll just ignore it.
Bottom line: keep formatting as simple as possible.