This may not be the answer you are looking for, but just to throw it out there....
iGoogle has a
simple portfolio tracker.
For each account, you would just create separate portfolios.
You'll have to enter each funds for each portfolio (including duplicates). That information can also include the number of shares (which you'll have to update every quarter).
It can also track every transaction you've made if you want to use that feature.
It will do all the basic calculations for you and give you an easy bottom line.
After that, the share prices and portfolio total will be updated for you every 20 minutes.
Won't do any fancy analysis or pie charts or anything though. But my situation is pretty simple, and this freebie is good enough for me.