In the last few months I've been toying with cports, a continuation of the mpkg packaging system. The original version of mpkg had autoconf and automake as a part of the basic configuration of the system. This somewhat made it easier for the basic system to be setup by less advanced users. cports had removed this functionality so it could be packaged up pretty simply as an rpm for caoslinux, while this is well defined and usable for caoslinux it wasn't as useful for me.
After digging around for some autoconf and automake replacements I found these...
I eventually just chose to use Configure even though it had no basic checks for C++ or Fortran. It's pretty self contained and small, there's enough bits and pieces there for small projects to add new checks to the system. It's certainly not as powerful or full featured as some of the above listed tools. One of the main problems of the other tools is the requirement for them to be pre-installed on the machine that you wish to run the configurator on.
On the other hand Configure is just written in sh, it'll pretty much run on any UNIX like system, but it's probably never going to work well on windows. waf looks interesting enough for me to take a look at somepoint, it's almost as light weight as Configure except it requires python to be installed. For now Configure suits cports just fine, it small, simple and pretty hackable.