This actually was a huge issue for me which convinced me to get an Ipad.....But I still do have a kindle 3 coming so I hope Amazon continuously improves their software
Im sure a programmer could possibly create an app and somehow use that clippings.txt file to convert it to its associated pdf ? The biggest deal for me is when I take all those notes and bookmarks they are just inserted into that text file.....When I go to open the pdf in the computer or another device all my notes and bookmarks arent there......
Here is a link also that talks about it some more it is nearly a year old but the information is still relevant ..... ::
http://www.threadpartners.com/blog/?p=47
You would think they would have tried to improve on this by now