Is there a way to tell automake not to interpret part of the automakefile?

The reason automake does conditionals is because some dinosaur makes don't. That said, if you really must do this, you could define your snippet as a variable in configure.ac and AC_SUBST it into your Makefile. That way, automake won't get a chance to see it. Remember to use AM_SUBST_NOTMAKE to avoid creating a line like FOO = @FOO@.)

dnl In configure.ac:
snippet='
ifeq ($(somevar),Y)
foo
endif
'
AC_SUBST([snippet])
AM_SUBST_NOTMAKE([snippet])

and:

## In Makefile.am:
@snippet@

I sincerely hope there's a better way than this.

I managed to find a different solution. You can put your to-be-escaped bits in a separate file and then do:

$(eval include $(srcdir)/Include.Makefile)

Since automake doesn't understand $(eval it just leaves the entire line intact. Thus you can put whatever you want into the other file and GNU make will happily read it. Note you can't just use include directly since Automake does understand that and will go into the other file.