In an autoconf/automake/libtool project you need to run:
libtoolize: this copies/links a few support scripts, including ltmain.sh (which is the main component of libtool).
aclocal: this looks up all m4 macros that your configure script will need, and make a local copy for easier access.
autoheader: optional, if you want to use config.h/AC_CONFIG_HEADERS, otherwise all the test result macros will be inlined when you call the compiler.
autoconf: to expand all the macros used by configure.ac into the configure script.
automake: to convert all the Makefile.am into Makefile.in templates. You probably want to invoke this with --add-missing so additional support scripts can be linked/copied to your project (such as compile, missing, depcomp, test-driver, etc).
Don't worry about running each tool. Just invoke autoreconf -i and it'll run the tools that are needed. Add -v if you want to see what tools is being executed. To avoid mistakes, just put a script like this at the root of your project:
#!/bin/bash -x
mkdir -p m4
exec autoreconf --install "$@"
Users that checkout/clone the project directly from the source repository will need to run this ./bootstrap script at least once. This is not needed if the user got a tarball distribution.
Automake can take fairly good care of itself; it'll re-invoke the above tools when needed, when you run make. But if you generate a broken Makefile, you'll need to invoke ./bootstrap and ./configure again to generate new Makefiles.