OK definitely getting a 15" quad core with Matte high resolution display and at least 128GB SSD drive. Now the question is what other upgrades:
2.0ghz -> 2.2ghz? or
4GB -> 8GB RAM? or
128GB -> 256GB?
or none of the above. If I do any *real* computations I will use more office machine or the departmental server. Then the programs I use most are Adobe Illustrator, Texshop, SAGE for small computations (ones that aren't going to run for days), NeoOffice, possibly Aperture in the future for photo editing, and of course Chome, Mail, Preview or Skim and Itunes are always open.
I am thinking 2.2Ghz processor, 4GB RAM, and 128GB SSD (I can always upgrade the RAM and HD later). I may have to get Applecare because it will be a university owned machine. I am not sure that I will be allowed to replace the HD or RAM on my own also (because it will not technically be my machine) so that should be something to factor in. Maybe I don't really need the 2.2Ghz processor though.
Also, I am keeping all my music and pictures on an external drive and don't plan (at this point) to put Windows on the new machine so I think I could get away with a 128GB drive.... I would get the 256GB SSD but it is so damn expensive!