created by some mad scientists at AT&T, this open-source script is capable of performing feature detections in a way that is much more simpler than Autoconf could ever dream of. A really good document about it is there, and you can also read its man page here.
The IFFE interpreter itself is nothing more than a portable shell script known to work on all flavors of Unix. You can put it in your CVS because it will never change. You don't need to touch it at all because it will read small "probe" files containing instructions regarding the features you want to test. The output is trivial to include in a Make-based build system, and can work with pkg-config too.
One nice "feature" that IFFE doesn't have is the ability to select feature through switches in a "configure" script (e.g. --prefix=XXXX --disable-static --disable-debug, etc...)
pmk (a.k.a. Pre Make Kit)
this is something completely different, designed by some programmers that were completely fed-up with the Auto-tools. They designed a small language and interpreter to deal with most features they needed, with 10 times less complexity. They even have some nice partial Autoconf compatibility to make transition easier. Unfortunately, they don't even support Windows (even on Cygwin !!), which sadly makes them totally irrelevant for real-world usage (IMO).
While these are not perfect solutions, they prove that it is possible to make simpler tools to deal with these issues. My understanding is that people don't want to learn a new installation procedure. All they want is type "configure" with their usual parameters then launch make (and why are we still using Make in the 21st century eludes me :-).
If a viable alternative appears, it will need to provide similar commands.