How have you tweaked the MATLAB environment to better suit your needs? One tweak per answer.
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I use a function idetitle() that can change the window title of the Matlab GUI itself. Useful in a development environment where I'm running several Matlab processes, possible on different branches of source code or model runs. Sometimes I'll put the PID in the window title to make it easy to find in Process Explorer for monitoring resource usage.
send the outputs to your email esp when the running is long http://www.mathworks.com/matlabcentral/fileexchange/29183-sending-reports-and-timestamped-file-by-emailing
create a result collector for archiving and sending http://www.mathworks.com/matlabcentral/fileexchange/29255-track-collect-and-tar-inputs-and-outputs
a patch to line up the file within a directory in proper order http://www.mathworks.com/matlabcentral/fileexchange/29033-file-ordering-patch-utility-for-matlab
I have functions to 1) save the current figure locations and sizes on the screen, and 2) and one to load such configuration. It's very useful e.g. when monitoring data-heavy simulations.
I implemented analogues of xlim and ylim: xlim_global([xmin xmax]) and ylim_global([ymin ymax]), which sets the axes' limits the same for every subplot in the figure.
I set shortcuts for
Ref: http://www.mathworks.com/matlabcentral/fileexchange/19097-custom-panzoom-icons
I keep a diary for each session (possibly multiple diary files per day) to recall all commands executed. This is controlled by a startup.m file that checks for previous diary files from that day.