EMSegment appears to be breaking the build on linux.

What is the error ?

Linking CXX executable ../../../../bin/qSlicerAppCxxTests
/usr/bin/ld: cannot find -lvtkSlicerEMSegmentModuleLogic

I tried commenting out EMSegment from SuperBuild.cmake but that didn't help.

Strange. Did you do a clean build ?
the dashboard show up clean .. see http://slicer.cdash.org/buildSummary.php?buildid=178456

Simply commenting EMSegment won't do it, the associated option need to be disabled. Otherwise, the library will still be expected. See [1]

If you do a build from the top level including EMSegment, do you confirm that the following text appear when the Slicer inner project is configured:

[...]
-- Configuring SEM CLI module: EMSegmentCommandLine
-- Configuring SEM CLI module: EMSegmentTransformToNewFormat
-- Configuring Loadable module: EMSegment [qSlicerEMSegmentModuleExport.h]
-- Configuring Loadable module: EMSegmentQuick [qSlicerEMSegmentQuickModuleExport.h]
[...]

[1] https://github.com/Slicer/Slicer/blob/master/Applications/SlicerApp/Testing/Cpp/CMakeLists.txt#L33

It seems that a clean superbuild is in order because the BUILD_EMSegment option does not show up in cmake, whereas in a new build directory it does.

Sounds good. Keep me posted of your findings.

Maintaining this extension implies some work (mainly related to keeping tcl/tk support in good shape). Building EMSegment as an extension wouldn't remove the burden associated with the tcl/tk maintenance.

Do we really need TCL? It should not be difficult to port TCL code to Python.

Do we really need TCL?

My understanding is that there is EMSegment "profile" or "task" definition implemented in Tcl.

It would be worth checking with Kilian if this still applies.