From a few recent posts I got the impression that at least some people assume that, if you have a magical focus covering a particular item (say, wooden wands), then your focus applies to your Lab Total whenever you enchant that type of item.
In our troupe, we've always assumed the focus applies only when the item is the target of the magical effect (e.g. a wooden wand that can turn into an asp), or is similarly tied to the magical effect (e.g. a wooden wand that turns animals into wooden wands). We've also allowed the bonus to apply if the magical activity primarily involves "priming" or "bonding with" the item (e.g. a focus in spirits applies if you are trying to bond with a spirit familiar).
We've never allowed the focus bonus to apply to every effect instilled into the item. E.g. a focus in wooden wands does not apply to your Lab Total when you are trying to enchant your wooden wand with The Incantation of Lightning. Similarly, a Verditius with a focus in wooden wands does not gain any bonus to his Lab Total when enchanting a wooden wand as a casting tool for The Incantation of Lightning (though he would gain the bonus if he had a focus in storms or damage). And a magus with a spirit familiar and a magical focus in spirits does not get the bonus to every effect he instills into the bond.
How do you play it?
(EDITed for clarity)