This requires using scripts, but there is a script that allows you to make giant enemies. Use one of these scripts to make giant goombas. You can even have them split into normal size goombas when defeated.
You could make the hyper goombas from Paper Mario. Without scripting, I would make them more like ropes. With Moosh's Newbe Boss script, I would give them the charge attack.
You can make the flying goombas from Mario 3. Make one that moves like a vire. Make another that moves like a bat.
You can make goombas with the spike helmets that are immune to the stomp boots. Maybe up their attack and hp as well. Also make hyper versions of them.
While not a goomba enemy, you could have a goomba that, when defeated, transforms into Zoroark. Here is the reference.
You could use the goomba in the boots from Mario 3. Just make them move like polsvoices or vires. When defeated, they are out of the boot.
You can use tanuki suit goombas that will turn into stone and back again. Without scripting your would make 2 enemies. One is the goomba with the tanuki suit and the other is the stone goomba. Both of them will have tribble as their death. They will just tribble into each other. The stone goomba will be immune to everything and have a walking speed of 0.
You can have a mama goomba with a bunch of baby goombas move like a lanmola. This could also work in patra form as suggested by Jared.