Since you insist on doing this using a Custom Number Format, here's a nifty trick you can use:
Enter the numbers and use the following as the custom number format:
This is what you'll see:
So close, right?!
This is where the trickery comes in. There's no easy way to hide the percent symbols, but here's what you can do. Open the Format Cells dialog again and position your cursor between the second comma (reinsert if it has disappeared) and the first percent symbol, like so:
Now press Ctrl+J and you'll see this:
As you can see, the three percent symbols have magically* disappeared! However, when you ok your way out the cell contents will still look exactly the same as before, so what did this achieve? Patience, my young Padawan... :)
Select the column with the numbers, open up the Format Cells dialog once more, go to the Alignment tab this time and select the Wrap text checkbox under Text control:
Ok your way out and boom!
* All right, you got me, it's not magic. But how does it work? Apparently, Ctrl+J inserts a Carriage Return into the custom number format text field (how non-obvious is that?!). You can confirm this by using the down arrow key after that sequence, and you might just be able to make out that there's another line of text there with the three percent symbols.
Now you can probably guess the rest. Enabling text wrap just wraps the text in the cells so the percent symbols drop to the next line. But if you don't resize the cells to be bigger in height, they still look like they have only a single line of text in them. Sneaky, no? :) Here's what it looks like if you increase the cell height:
Note that the actual values in the cells are still 1, 12.3 and 123456.789 respectively, only the way they're displayed has been affected.