I like the eyeballs option for skeletal undead:
Firstly, let's face it, this is necromantic magic at play. So what if the skin's gone? Their ligaments and tendons and muscles are gone too, but they can bloody tap dance on a bar top if they want to!
Secondly, the effectiveness (to me) of actual eyeballs lolling about in a bony skull is startling and evokes the truth that this thing was once alive, once a person of flesh, blood, and eye. Dry bones might be scary, but glistening, rotted flesh (or better still, a clean white unblemished eyeball!!) speaks volumes.
Just my opinion. Eyes? I vote aye!
JFK