I use my iLiad for the purposes you describe (I'm a graduate student myself) and I'm quite happy with it. PDF support is very good. Searching text within non-PDF files is supported with FBreader. Searching text within PDF files is still a work in progress, though the community developers are looking into it. The iLiad supports multiple fonts, but does not ship with the non-Latin fonts, so you'll need to install those. (If you have a Japanese file you'd like me to test, I can do that. I don't have the energy to dig up a Japanese PDF myself right now.) Since the iLiad uses Linux, you can create symbolic links to files, which I think would give you the "playlist" sort of feature you mentioned, though you'd need to use a shell or file manager to do it.
There are also a number of very good expanded PDF viewers developed by the community that offer extra features, such as column navigation or the ability to mark and extract excerpts.
I was able to buy my iLiad second hand for a good price, but that was right after the Sony Reader was introduced, and many people were switching. Still, you might check around and see if you can find one used from someone you can trust. (I bought mine here from a member who'd been around for a while.)
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