This seems a rather silly question: but I can't find (for more than an hour) now a button to "reset" all standard windows.. I accidentally closed quite a lot of them during a crash. (Especially the "command window" and the signals-in-region during simulation seem to be gone permanently).
From "ModelSim User’s Manual, v10.1d", appendix F:
Most user GUI preferences are stored as Tcl variables in the .modelsim file on Unix/Linux platforms or the Registry on Windows platforms.
You may consider to look into .modelsim, and possibly delete it, together with .modelsim.bak. The motivation for this suggestion is that .modelsim contains setup details for the layout of panes. .modelsim will (should!) be regenerated next time you open modelsim.