The instructor should be able to define a set of fields, some to be imported, some to be calculated, and some from internal sources (quizzes or whatever) that students will be able to see.
It should be easy to import CSV files with student numbers in one column and scores in another that will be matched up appropriately. It should be easy to point a new imported row at one of the fields in the spreadsheet. It should be hard to delete or overwrite rows.
The instructor should be able to select and unlock multiple rows of data given a variety of search parameters
When data is modified there needs to be an audit trail.
There are quite a few grading apps out there but few of them export to the web or to CSV... There is a growing demand from users for grades online functionality...but there is also an ongoing battle over grades online out of fear of being hacked.
Keep in mind the handhelds as well; the gradebook interface should be configurable for a tiny interface. I like to walk around and check off students homework. I want to be able to show them their grade right then and there.
could be nice to be able to grade forum posts directly to a specific part of the gradebook (see RFE)