Scons - an autotools replacement and chrome's build tool
scons.org
scons.org
I've always used Make because it's what I know, it's what the Linux/Unix community tends to use for the majority of projects, and because I don't fully understand the competitors products. However, I've been bitten in the past by quite a few restrictions in Make, but every time I look into the alternatives, I see very few similarities with which to make a comparison judgment, and it seems more practical to just stick with what I know and work around the flaws than to start from scratch with something else that may have just as many limitations as Make...
http://lwn.net/Articles/188693/
I find QMake, even for projects that don't use Qt, really nice for projects that don't need to be packaged up or have complex dependancies. The format is trivial and it does well with generating makefiles, XCode projects or Visual Studio projects.
AFAIK, either make or vanilla jam is the fastest for C++, which is by far the most important thing to me, but that'll vary depending on your particular situation.
This is a bit old, but still accurate: http://www.gamesfromwithin.com/articles/0509/000100.html