I'm pretty sure 'shoot 'em ups' or shmups are games like Raiden, Ikaruga, 1942 etc. Metal Slug I think is in the 'run n gun' genre.
So my favourite shoot em ups in mame are Raiden, 1942, Bells n Whistles, Zero Wing.
For run n gun my favourite would have to be Commando. Metal Slug is bloody excellent too, but not so great on my cocktail cab. On an interesting side-note, I'm pretty sure Commando, a run n gun, uses the 1942 'engine'. Funny how doing almost the same thing, but substituting a P38 Lightning for a commando, changes the genre...