This is a fairly simple idea: branding irons, which would be used to name mobs, in a similar fashion to nametags.
Branding Irons would be crafted like so:
The resulting tool would have durability of say, 100 uses (Or something like that), and would be used by right-clicking a mob. If the mob is nameable, a text box would appear, in which you can type the creatures name. The Branding Iron would be repairable with iron ingots at an anvil.
Yeah, thats really it, thanks for reading.