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To convert PDFs to anything the best tool I have found is ABBYY PDF Transformer. At $99 it will convert text based PDFs (like those made with Word) as well as graphic based PDFs (such as scans) to RTF files. I can then use these files as they are or convert these files to HTML (3.2, never 4), DOC, TXT, or whatever format I need for their future use. I keep a copy in RTF as I like to have a copy as close as possible to the original source. (Disk space is cheap these days and I can always burn a CD or DVD of the project later.) Once I have cleaned the file (to correct OCR errors for example), I may delete the work files. Sometimes I keep these if I feel that I may someday revisit the files to do more work on them. (For example I keep threatening to revise the Harvard Classics to correct formatting error that others or I have found since they were published. Nick has offered to convert these to the multiple forms of IMP for me when I do complete the next series but I am still backlogged and this has just not come to the surface yet.)
As Nick mentioned, PDFread should be a last resort. I have used it a few times for things that I wanted to read but not keep or convert. To me ePub sounds nice but I have no use for it as my reader does not support it. I do keep the LRF of many of the files I create; however, I view it as a terminal format rather than one that I would use to archive or create other things from.
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