If you start Blender with blender -w it will run in a window.
-w Force opening with borders
-p <sx> <sy> <w> <h>
Open with lower left corner at <sx>, <sy> and width and height
Type ‘man blender’(without quotes) into a terminal, it should give a list of other command line options.
There should be a utility somewhere that allows you to configure what applications are displayed in the Applications menu. On Ubuntu (Gnome) it is System => Preferences => Main menu. You can left click on an application’s menu entry, and for Blender, change its properties from ‘blender -W’ to ‘blender -w’.