I agree that MOBI and EPUB are the two best choices.
EPUB's pluses:
- Its an editable format making fixes and adjustments possible without requiring conversion to another format first.
- Its a very popular format making the likelihood of future support very good.
- It supports a very wide range of formatting options
EPUB's minuses:
- It supports a very wide range of formatting options, many of which are not supported by other formats thereby causing the occasional poor formatting when converting to other formats when some EPUB function is not supported in the target format.
MOBI's pluses:
- Its a very popular format making the likelihood of future support very good.
- Its has a lot of formatting options, though somewhat fewer than EPUB and thereby less likely that conversion to another format will result in issues.
MOBI's minuses:
- Its not an editable format so when a conversion from MOBI results in a formatting issue you can't edit the MOBI to address the issues and reconverting. You must convert to some other editable format (e.g. EPUB) to make the fixes before converting to the desired final format.
Personally, I archive primarily MOBI format. That primarily because Mobipocket Reader has been my reading software for over a decade. I now use a Kindle, but used Mobipocket software on a Windows sub-notebook and two Sony Clies, previously, after migrating from an HP320LX (WinCE v1.0 & v2.0) and its DOC format.