Since version 1.1 it's possible to configure which buttons do you want to use in the toolbar of Writearea. There are in fact two toolbars and you can switch between them with a custom button.
The way to define the buttons is to use the preferences pane of Writearea and put the array of buttons in the corresponding input fields. Note that to try to help a little, you don't need to put the outer [ and ], just the groups separated by commas and with a '/' if you want to start a new row.
These are the default values for each toolbar:
['Save'], ['SaveFile','LoadFile'], ['Source'],['Cut','Copy','Paste','PasteText','PasteFromWord'],['Undo','Redo','-','Find','Replace','-','SelectAll','RemoveFormat'],['ShowBlocks','Maximize'],['Image','Flash','Table','HorizontalRule','SpecialChar','Iframe'],['JustifyLeft','JustifyCenter','JustifyRight','JustifyBlock'],['BidiLtr', 'BidiRtl' ],'/',['Styles','Format','Font','FontSize'],['Bold','Italic','Underline','Strike'],['TextColor','BGColor'],['NumberedList','BulletedList','-','Outdent','Indent','Blockquote','CreateDiv','Code'],['Link','Unlink','Anchor'],['SwitchToolbar']
['Undo','Redo'], ['Bold', 'Italic', '-', 'NumberedList', 'BulletedList', '-', 'Link', 'Unlink'],['SwitchToolbar']
Most of the commands are the ones available on the default CKEditor install, I don't know if there's any listing of the meaning of all of them, the best thing that I can think of is the user's guide, but it doesn't clearly link the button names with its action.
But beyond those common buttons, there are a few ones with special meaning here:
'Save': It's available only while in the dialog popup, it will save the content of the editor to the original element. When the editor is integrated into the page you should use the existing save button provided by the page, that way there won't be any problem due to extra event handlers or differences between Save draft, Publish and Preview buttons of the page.
'SaveFile', 'LoadFile': These two options allows you to save/load the content of the editor to a file in your computer, just in case the page doesn't have any auto-save feature or you want to use something more than once.
'SwitchToolbar': These button allows you to switch between the basic and the full toolbar. I would suggest you to use the basic toolbar by default and only switch to full toolbar when there's something extra that you need at that moment. And of course, adjust each toolbar so the basic includes the commands that you usually need and the full toolbar doesn't includes buttons that you know you'll never use.
'Code': it's the SyntaxHighlight plugin available here. I made some little adjustments, but someday I might have to perform some bigger fixes to improve it and make it easier to use.