A few years into the future...
- SCons is dying off in popularity, from what I've seen. I don't like it at all.
- Waf is awesome (in my opinion). If you're looking into SCons, try Waf first. However, parallel builds always show you all the errors that occurred...so expect your screen to be flooded with error messages. Also, it can get a little complicated to extend.
- Boost.Build is one of my favorites but has the worst documentation on earth. Other than that, it's very flexible and lets you do almost anything. It can be a tad slow at times, though.
- CMake is good for only generating Ninja scripts; anything else is garbage (4000 lines of makefiles for a 1-source 1-executable project)
- Tup is nice, but it lacks anything for configuration.
- Autoconf is still autocrap.
Other ones not mentioned:
- Kbuild is a tad weird but looks nice. That's all I know.
- mk-configure is great for make lovers.
- Shake with shake-language-c is flexible and lets you do anything...if you know Haskell and don't mind abandoning VS support.
- Jamplus loves to shove
-m32 at the end of every freaking compiler command, which sucks on a 64-bit system.
- Tundra can be a tad repetitive but is still very fast and accurate.
- Bam...Tundra is better. It's fast without sacrificing accuracy.
- Gyp (used for Google Chrome/Chromium) is underdocumented but is a great alternative to CMake.
- Premake is great if you value simplicity, but it can get annoying when it comes do doing seemingly simple things.
- Bakefile is very restrictive but great for simple projects.
- fbuild is my favorite (along with Boost.Build). It's quite underdocumented but has plenty of examples and very readable source code. Build scripts are short, too. It's used to build (and was designed for) Felix. It's also very, very fast, and it's almost always perfectly accurate and has automatic parallelism that DOESN'T flood your screen. Ever. I'm using it to build a regex JIT engine and am very, very happy. It's also very easy to extend. However, it's still technically in beta, although I've never experienced any real problems.
I'd recommend fbuild or Boost.Build...or Gyp if you like makefile generators.
If you want to extend the basic functionality, definitely use fbuild.
If you have LOTS of platform-specific flags/options and plenty of messes, use Boost.Build.
If you need a makefile generator or have lots of configurations, try Gyp.