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For optimum viewing options, I'd use ePub. I don't mind ragged right edges, and ePub is more convertable to other filetypes later if I care about it. I consider LRFs to be throwaway files--read and delete; keep something else for long-term use options.
If I had to chose one for a purchase, it'd definitely be ePub.
For a lot of my reading, I'm prone to converting things to custom PDFs sized for the Reader. (For free PDFs from the various publishers that offer them, I tend to add tags, which greatly helps reflow, and bookmarks, after which they're much less painful to read.)
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