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The best archive formats are the richest in features. So the best in the future will be ePub, but there aren't enough tools for ePub creation or conversion yet.
The best today is OEB, which almost no reader reads directly (the exception is FBReader) but that is what LIT and MOBI are based on. MOBI is not a good archive format, because MobiPocket Creator starts with an OEB ebook and converts it to MOBI - it won't even take a MOBI as a starting point because it is a "reader" format not an "archive/source" format. On the other hand LIT is a very thin wrapper round OEB, and ConvertLIT can explode LIT to OEB. This is why LIT is still the best format for DRMed ebooks, even though MOBI and eReader are both now also crackable. OEB is essentially html, images, and a .opf file. So HTML good too. If you have any multi-format ebooks (e.g. from Baen or FictionWise), I suggest archiving the LIT version (just in case) and then downloading their Sony version.
Absent good ePub tools, I would be inclined to archive your existing ebooks "as is". This definitely looses no information, and perhaps better conversion tools will exist in the future. This is particularly true of PDF, I don't think you loose much by converting RTF and DOC to HTML today.
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