As long as the spell hasnt shot yet, like to use your example Caitlyn's ultimate. if shes aiming her shot and hasnt shot the bullet, you can apply the extra damage as long as you can do it before the hits the enemy. As the damage isnt applied until the target is hit, any buffs or anything like that calculate when the champion is hit as opposed to when you start casting a spell. Thats what makes sense to me, and its what ive noticed from playing Nunu support, casting blood boil on my AD carry it immediately boosted his stats from when they auto attacked or casted a spell that my buff granted them immediate damage.