> Now, autotools/automake are a different (bad) story
While autotools are a bit hairy for the developer, the autotools-based builds usually work quite nicely. I regularly build the GNU toolchain (gcc + binutils + glibc) for cross compilation and usually it works like a charm. I grab the sources from git repos so naturally they have their moments, but it usually works better than any other build system.
Some build systems are a lot more convenient for simple tasks (I like CMake) but when it comes to cross compiling or truly configuring for varying build sites, autotools-based systems deliver.
A few years ago there was some hassle with autoconf/automake version numbers but that seems to have been solved now.
I (usually) don't have a problem with Make, I think it's a good tool for what it does (basically, a DAG solver)
For all means use make with hand-made files.
Now, autotools/automake are a different (bad) story
The alternatives posted here are very interesting