I have a generator program that creates two version files, say ver.h and ver.cpp. My ultimate build target depends on both of these files, and the rule
Using the phony target as the prerequisite is a bad idea. program will be run even if ver.* files exist, which is a false positive error.
More subtly, GNU Make is only guaranteed to update its file timestamp, if that file is a target of a rule with a recipe. So here, even though program is always run, anything that in turn depends on ver.* files might not get updated at all!
In my opinion it is best to not make up unnatural patterns for each target, but instead, go explicit:
There is a "main" file that you are generating, that is ver.cpp. Use the "no-op" recipe ; for the other one, which can be put on the same line like this:
ver.h: ver.cpp ;
ver.cpp: Makefile
./gen/version/program
This method starts with what you wrote, but adds the very important ;.
If you did not have a natural candidate for the "main" file, then in my opinion it is best to use a "sentinel":
ver.h ver.cpp: sentinel ;
sentinel: Makefile
./gen/version/program
touch $@
Again, this method is similar to one of your methods, but very importantly, does not use a phony, but a real file.