I know you can smelt some of them into dwemer ingots, which I have done, but I have some dwemer things left like cogs and various other things that I can't smelt. Should I just throw them away or are they used for something else?

Dwemer cogs are needed for a quest. The other stuff can be melted down to dwarven metal

Hmm, I can't melt the bowls and some of the other dwemer stuff though.

Ya the bowls and the other stuff are just decoration and junk

Go to Wilhelm and melt them down at the blacksmith shop. I always collect them for this reason.

I believe Dwemer stuff that is labeled either "large" , "small" , or "bend" can be molten into ingots.
Not sure if any other, but pretty sure about these.