Do you use a master ball on Ho-oh?

It depends on if you want ho-oh right away and don't have the time to weaken it, you can if you want but i would recommend using it for Lugia if you can catch it in gold. Hope this helps =P

I would recommend that if you are using the Gold version, use it for Lugia (since it would be level 70 while Houou I think is 40 when you catch it), and for Houou in the Silver version (since if then, Houou will be the level 70 Pokemon)

But personally, I would use it on a legendary dogs. They are much harder to catch because they escape you a lot, unless you have a move like Spiderweb or Mean Look equal to or under Lv 40 (Crystal) or 50 (G/S) to use a repel in a place w/o Pokemon in the aforementioned level range.