Mentor Grpahics Calibre has a very good interface written in Tk. Also some utilities from the Encounter suite have Tk interfaces (not the whole suite of course as Tk is not suitable for graphicslly intensive applications)
The other thing I use Tk for at work is writing test scripts for hardware. Often the hardware has a serial port or an ethernet connection in it somewhere. Tcl includes serial port support, and also has an event loop that supports callbacks for both serial port and sockets. I don't think _any_ other solution beats Tcl/Tk for this type of thing. In a way, it's a shame so few people know about Tcl/Tk these days ...
For my modelsim scripts, I usually incorporate a menu in the main modelsim toolbar for my projects. The menu will incorporate menu items for things like library compile, rtl compile, testbench compile, listing all available testbenches for selecting and running. Usually my menu will be organised using submenus. That sort of thing is very quick to do, and it makes developing RTL a little less painful.