Can anyone tell me what the difference is between a Beretta 687 EL Gold pigeon and the 687 Silver pigeon?

Cosmetics. The EL will have sideplates added and (theoretically) a higher grade stock. Mechanically, they are identical.

I have owned both, and Bluestem is correct.

So the only difference is the gold dog and birds correct? Can any one tell me the value of a NIB 410 Gold pigeon made in the late 90's?

I would guess $3000ish. A gold pigeon is fitted with side plates where a silver pigeon is not.