I'll add a couple things about schlepping stuff back and forth between two offices:
1. Have just as many of the travelling folders as you need. I'm a medical student (who's school is 30 miles away from home and who lives out of her car), and mine are:
--Inbox
--Action support (for those one-time pieces of paper: support info for a phone call, basically for paper that I'll need that doesn't have it's own project folder)
--Return to Home (where all my reference files are)
--File for class: I figured out I needed a place to hold stuff until I made it to the super-duper hole punch to put holes in the 40 page packets.
Now, of course, what I call my folders won't matter a bit to you, but it's important to make them work for you. (I don't know how long I carried around a Read/Review folder totally empty before I figured out it was just bothering me because I don't really have anything in that category.)
2. The best tool I bought for these folders is a "file pac" (or something similarly named) from Levenger. (They have a "travelling Inbox" that is similar, but it was too big for my bookbag. YMMV.) I actually bought two, in different colors: one for the folders listed above, and one for the few project folders that I lug along with me sometimes. For me, it's nice to have those separate. If you have a traditional briefcase, you may not find these necessary, but they're a godsend for me. Plus, there's a place for post-it's and paperclips so that I have those with me, which makes using the folders easier.
3. Don't be afraid to put the dumb things like "empty office folder" on your @Office list. I have a few of these things (Punch notes in ERC) on my lists, and it really helps me stay sane organizationally. If you're better at habits than I am, dumping everything as soon as you get to the next place might not be such a big deal, though.
--Sara