When installing vavoom, I get the following errors:

test -z "/usr/pkg/share/vavoom/basev" || install -d "/usr/pkg/share/vavoom/basev"
install -c -m 644 'common/basepak.pk3' '/usr/pkg/share/vavoom/basev/common/basepak.pk3'
install: /usr/pkg/share/vavoom/basev/common/basepak.pk3: open: No such file or directory
install -c -m 644 'doom/basepak.pk3' '/usr/pkg/share/vavoom/basev/doom/basepak.pk3'
install: /usr/pkg/share/vavoom/basev/doom/basepak.pk3: open: No such file or directory
install -c -m 644 'doom1/basepak.pk3' '/usr/pkg/share/vavoom/basev/doom1/basepak.pk3'
install: /usr/pkg/share/vavoom/basev/doom1/basepak.pk3: open: No such file or directory
... (etc)

The directory /usr/pkg/share/vavoom/basev got created by the installation, but the intermediate directories (doom, doom1, doom2, hexen, strife, tnt, plutonia) are not created. See the first line: there are only directories up to the basev created, not the ones below. install doesn't get a -d flag to tell it to create any missing files underneath. I don't know enough about Automake to supply a patch, but it looks like this is caused by the fact that the directory is declared

basevdir = $(datadir)/vavoom/basev
nobase_basev_DATA = \
        common/basepak.pk3 \
        doom/basepak.pk3 \
        doom1/basepak.pk3 \
        doom2/basepak.pk3 
... (etc)

Automake sees the entries under nobase_basev_DATA as files, while they also contain a directory component. A solution would be to move the Makefiles into every subdirectory and let them all handle their own stuff, perhaps.

Yes, that's the best solution.