Upgrading the autotools (autoconf, automake) is not difficult, you just have to remember to update all the key packages.  I’ll be using the portupgrade command to update the autotools.
First, let update our ports tree:
# portsnap fetch
# portsnap update

Now the autotools themselves:
cd /usr/ports/devel
# portupgrade -r autoconf
# portupgrade -r automake

And finally two key packages that will allow the other ports to see the new versions:
# portupgrade -r autoconf-wrapper
# portupgrade -r automake-wrapper

if you don’t upgrade the autconf-wrapper and automake-wrapper ports, you’ll see errors such as this when you try to perform other port upgrades:
autoconf: required version 2.68 not found
even though you have upgraded the autoconf port.