Small companies = ok to call.
Big companies = you're a small pain in the arse if you follow up by email, a medium pain in the arse if you call once and a BIG pain in the arse if you call more than once.
Large companies have procedures in place for resume handling, and asking them to go outside their procedures is just a little annoying. Doesn't make you look motivated, just makes you look like you don't "get" how the corporate world works. So you can if you want, just use with caution.
Also note: if you've been applying to lots of roles at the same large company it will show up big and bright when they look up your name; makes you look unfocused and desperate. Better to selectively apply, especially if you intend to follow up.