There's a number of things I'd like to have my machines do outside of making items:

1. Placing blocks. This could lead to more interesting automation (the machine places its product in a designated place, rather than outputting into a neat inventory slot) or risky machines that have a chance of melting down (the machine runs an alternate recipe at 5x power input that puts out more stuff, but can also place lava nearby!)
2. Breaking blocks. This lends itself to more of that weird automation, or machines that can "break" and require check-ups and maintenance, and combined with placing blocks can lead to machines that change themselves (similar to a suggestion made for ModularDiversity: DaedalusGame/Modular-Diversity#10 )
3. Summoning entities, such as monsters. Imagine a machine like Half-Life 1's Anti-Mass Spectrometer, which produces valuable things...but if you overcharge it, it could cause monsters to be teleported all over your base! Alternatively, you could create a machine that takes in power and periodically creates a splash potion, or a machine which allows for mob farming.
4. Redstone control! Obviously you could have machines that toggle off and on when powered, but you could also combine this with breaking/placing blocks and multiple machine definitions to create machines that require a sequence of redstone signals to function, or a machine that outputs an increasing redstone signal as its core turns from iron to a magma block and finally melts down into lava.