Here's my updated list. I'd really appreciate it if anyone who knows how to do the things in this list with Version 3 would reply with an explanation. I checked all these reports out as well as I could, but I certainly could have missed something.
Function or feature or issue
Reorganize Panel gone, no multi-level sort.
Categories View gone
References now don’t follow sorted rows as they did before.
Table Fills are not supported
German user can’t use decimal points from numeric keypad.
Split Cells is gone
Sheet View seems to be the only view available during editing. Page view only available in the Print dialog.
Page Headers and Footers are gone
Edit Toolbar (add, delete, rearrange tool icons) is gone.
Scatter Charts no longer can accept Dates on X axis
Dates can’t be used for X-Axis values in Scatter Charts
Custom Formats gone
Ability to set margins gone
Cell border custom line weight is sometimes lost when using Filter Rows
Ability to sort selected rows is gone
Header text is used in cell references and you can’t turn this “feature” off
Can’t set Page Margins; they default to about 1” all around
Formula Bar is gone, replaced by a field at the bottom of the Numbers window in which the expression is displayed but can not be edited
Graphics Inspector no longer treats a Table as an Object that can be formatted by the Graphics Inspector tools
Comments only display as Tool Tips now, can’t be static displays
Can’t open Numbers 08 documents