When I run Matlab on a netbook with a tiny screen, I remove the statusbar and menubar of the docked command window. The editor is maximized also and all other windows are created on demand only, which is very rare: I access the current directory popup programmatically, Matt Fig's WHATS helps also, the history by the arrow keys, the workspace browser is retired, because all variables are stored in the GUIs or on the disk.
Well, I admit it does not look cool, especially with the classic scheme in Windows XP:
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