When I have compiled PETSc i've just done the usual "./configure; make", but since I had CMake installed and available in $PATH, it was used automatically.
The "NightlyBuild" targets, etc, are mainly supposed to be connected to http://www.cdash.org/. If one sets up a dashboard, different computers would run the nightly build target and the dashboard aggregates the results (so, one nightly build coming from OSX, one from Linux, varying configuration options, etc.)
Basically resulting in something like http://open.cdash.org/index.php?project=calaTK
The targets appear automatically when I use CTest, so I didn't intentionally add them (and if we aren't going to bother with CDash, I'm sure its possible to turn them off).
I'm not sure if they are that useful outside of CDash. "make Nightly" will check out the latest version, configure it, build it, test it, and while doing so, print some basic information on screen, and write the detailed warnings and errors produced in a XML-file. (which is what is sent to CDash)
$ make Experimental
Site: debian
Build name: Linux-c++
Create new tag: 20121214-1715 - Experimental
Configure project
Each . represents 1024 bytes of output
. Size of output: 0K
Build project
Each symbol represents 1024 bytes of output.
'!' represents an error and '*' a warning.
.**********..**.*.*....**...*..**..*.............. Size: 49K
Size of output: 49K
0 Compiler errors
50 or more Compiler warnings
......
and then it goes on to testing (i will replace the build name with something more useful)
B.t.w, I didn't figure out any simple way to skip the cemhyd tests if CemHyd isn't compiled, and its off by default (since it introduces another dependency).