In Unity (if youre running Ubuntu 11.10, 12.04 or 12.10), emulating a virtual desktop makes Nexus even bigger.. in my experience, but Dritz is wise in the ways of linux. perhaps you could drag the window offscreen more, dunno.
I know the OP solved his problem already, but another alternative to WINE is to run Nexus on Windows inside a virtualbox (https://www.virtualbox.org/). It is, in my experience, the fastest way to run Nexus. While I'm currently using WINE I have in the past had great success with nexus in a virtualbox in ME compatibility mode on an install of XP.
Using scale mode in virtual box.. you could resize the nexus window (the os window to be more accurately) to any size you want
{Edited to mention I run Ubuntu 12.10 Quantal 32 bit, and use PlayOnLinux rather than the default installation of WINE}
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