Any choices that would normally be made when the spell in a potion comes into effect have already been made as part of the potion creation process. This includes any choices of targets because the target of a potion is always drinker. Thus I suspect that when Potions says that "the drinker still controls the effect," it means that any ongoing effect is still under whatever control the spell's effect allows its caster to have.
The biggest example of this involves spells that include as part of their duration the note that they're dismissible, like the spell invisibility. A drinker of the typical potion of invisibility (2nd-level spell at caster level 3), for instance, is automatically considered both the caster and the target of an invisibility spell, yet the drinker can take a standard action to dismiss the effect before its normal duration of 3 min. expires because the drinker controls the invisibility effect.
To be clear, the effect of the typical potion of cure light wounds is to heal the consumer of 1d8+1 hit points of damage. This decision has already been made by the potion's creator, and there's no alternative decision the potion's creator can make. Further, the potion's consumer isn't allowed to simply opt out of that healing when the potion of cure light wounds is consumed. (This is why they work on unconscious folks.) A potion's consumer is automatically and irrevocably considered both the spell in the potion's caster and its target.
(However, even an unconscious creature can opt to make a Will saving throw against a potion of cure light wounds just as a caster can—if she wants—make a Will saving throw against her own cure light wounds spell! For example, a GM may inform an unconscious PC that's being fed a potion of cure light wounds only that either the PC's entitled to a Will save against an effect or the PC can voluntarily fail a Will saving throw against the effect, the GM not telling the player the nature of the effect nor why the saving throw is necessary because the PC's unconscious! Although this is—for a fantasy game, anyway—realistic and strictly according to the rules, I suspect such GMs are in the minority.)
To address the other possibilities the question mentions, at its least powerful a potion of magic missile (1st-level spell at caster level 1) has the entry Targets up to five creatures, no two of which can be more than 15 ft. apart so that must be one creature—the potion's drinker—according to how potions work. There are no other decisions to be made with regard to the magic missile spell: its range is now known and its damage is now fixed, for instance. A more high-powered potion of magic missile (1st-level spell at caster level 9) requires of its creator but one extra decision: How many missiles? And that decision is fixed when the potion's created, and the drinker will be the target of all the spell's missiles. There's not even the option for the drinker to make a saving throw! (Needless to say, a potion of magic missile is often only funny once.)
Similarly, a potion of shocking grasp has the entry Target creature or object touched and, again, the potion's drinker is automatically the potion's spell's target, and there are no other decisions to be made, and, again, there's no saving throw permitted. The drinker of a potion of shocking grasp is simply dealt the spell's potion's damage. (Attention, shambling mounds: When attempting to heal downed party members who aren't shambling mounds, don't confuse your potions of shocking grasp with your potions of cure light wounds!)
