Finally, in Ubuntu 11.10 (Oneiric Ocelot), it is possible to stop windows auto-maximizing in the Unity interface if they are set to take up more than 75% of the display. Of course, support for this is not available directly (that would be too easy), but a simple software installation and configuration is all that is needed to achieve the goal.
The step-by-step instructions (courtesy of T.J. Crowder, AskUbuntu) are as follows:
(1) Install CompizConfig Settings Manager (CCSM) through the Ubuntu Software Centre.
(2) Run CCSM and filter for Ubuntu Unity Plugin.
(3) Select the Experimental tab.
(4) Set Automaximize value to 100% to completely disable auto-maximize (or choose a different value – e.g. 95% – if preferred).
Note that it may be necessary to reboot the machine to activate the new setting; however, once it is enabled, subsequent settings take hold immediately.
How to keep programs from launching maximized?