multiple states in cookies

This is an absolutely crucial feature. It is equivalent to the UCSC Genome Browser "Sessions" feature, which I have found very useful in the past for saving tons of analyses:

http://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html

The other advantage of that feature is that I can make a session "public" and send a URL, which encodes the session name in it, to my collaborators, who can then open it up and get a browser view (specifically, a set and ordering of tracks and maybe a specific genomic view). If they do additional analysis on my data, they can re-save the session as something and send it back or keep it. (Well, in theory you can fork sessions like this -- the UCSC implementation is a bit wonky.)

Alternately, session data can be saved to a file and I can e-mail the file. This is probably an easier way for JBrowse, since it avoids saving session info on the server and tying an URL to it.

I define a "session" or "state" or whatever as:

• The set of tracks that is open (this is especially useful if you generated a bunch of custom tracks using UCSC's Table Browser, such as filters of filters of genes or some such)
• Their ordering
• Their view settings (JBrowse does not yet have this -- in UCSC it would be things like "dense", "full", "pack" etc controlling the feature layout, also track heights, wiggle scaling settings, etc.)
• The initial view