Use a Custom format.
Select the cells.
Open the Inspector and choose the Cells Inspector button (42)
From the pop=up menu in the Inspector, choose Custom... (last item in the menu)
Drag two additional Integer blocks into the format box.
Type a left parenthesis before the first.
Typs a right parenthesis, then a space between the first and the second.
Type a space between the second and third.
Hover the mouse over the first Integer block, click the white triangle, and choose "Remove a digit" from the pop-up menu.
Repeat with the second integer block.
Repeat with the third integer block, but choose Hide Separator this time.
Results should be as shown below:
In the image, the number as entered (5555551212) can be seen to the left of the dialogue. To the right, you can see the selected cell (B2), and the formatted number.
The old Numbers will be on your computer unless you deleted it. Look in a folder called iWork '09 inside your Applications folder. Launch Numbers 2 (Numbers '09) and do what you used to do to create a Custom Cell Format. For example, you might want a nine-digit phone number to appear as (123) 456 789.
Save that document. To protect it from Numbers 3.0, make a copy of that document with a different name. Ensure that both your original Phone Number documents are closed (to protect them from that bully Numbers 3.0). Then Open the copy in Numbers 3.0. The custom format will be listed in Format Inspector > Cell > Data Format
Type a nine-digit number into any cell and format the cell with Format Inspector > Cell > Data Format > Phone Numbers.
Note: copying a cell with Custom Format in Numbers 2 and then pasting into Numbers 3 does not work. The pasted cell ends up as Text, and the Custom Format is not added to the Data Format list.