Well, I have this mostly working now. I can use jabref to manage my refs, I have a filter that makes it easy to create a manifest file that contains the author(s) in the title, paper title in the first line of the description and journal name and pages in the second line of the description so they look good and are easy to identify on the iliad.
I also have another export filter that creates symlinks, so I can select a group of refs, export to symlinks and move the symlinks to some work folder on the iliad. That way I can keep all my refs in one folder and have collections for particular projects in another that point to the original articles.
But when you have hundreds of articles and no bibliography manager on the iliad using the iliad search becomes a pain. So, I have installed
samba as shown recently (thanks ajnorth!) on the iliad and access it from my PCs. I have setup some scripts and registered these as external file handlers in jabref (this is much simpler than it might sound, it's like setting up file associations in Windows 98 or something) and the scripts themselves are quite simple. I then network my PC to my iliad and setup an article entry to do different things depending on which option is chosen. The choices are:
i) open and view the PDF on the PC
ii) Merge the PDF and scribbles and view on the PC
iii) Make a symlink in an easily accessible folder on the iliad so I don't have to search for it
iv) open the PDF directly on the iliad (via ssh)
(The last option works in that it opens the PDF and was what I was after in the first place, but I have trouble closing it afterwards and might have to give up on this approach.)
Here's a screenshot showing the choices. I might even try to make a video and put it on youtube if people are interested and if I can figure out how to do it (never tried youtube before).
Jabref is really nice. I am really getting to like it. At the moment I am liking the static and dynamic groups. And it looks like there will be a plugin for OpenOffice soon (it is already in the dev version).