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I'm pretty sure the answer is yes but I'm tired and I can't find a rule about it one way or the other. For example if an alchemist took feral and wings could they choose to create a mutagen that just boosted their abilties then when creating a new one to have turn them into a winged anthropomorphic owl and the a cat-person when making a third or would all three have to use both the feral and winged discoveries.
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Not an expert, but it seems that it depends on the discovery.
Mutagen discoveries:
Cognatogen (Su): The alchemist gains the ability to create a cognatogen, a mutagen-like mixture that heightens one mental ability score at the expense of a physical ability score.
Feral mutagen: Whenever the alchemist imbibes a mutagen, he gains two claw attacks and a bite attack.
So the alchemist can choose to make a normal mutagen or a cognatogen, but he always gains the claws and bite attack when imbibing a mutagen (and the cognatogen, I would say).
The Cognatogen would have benefitted from a text like the Fey Mutagen: "The alchemist gains the ability to create a fey mutagen", making clear that the Conatogen is a mutagen for all the effects.
Other discovery
Wings (Ex) (Ultimate Magic pg. 18): The alchemist gains batlike, birdlike, or insectlike functional wings, allowing him to fly as the fly spell for a number of minutes per day equal to his caster level. These minutes do not need to be consecutive, but they must be spent in 1-minute increments. An alchemist can select this discovery multiple times; each time he does so, he adds his caster level to the number of minutes per day that he can fly with the wings. This flight is an extraordinary ability. An alchemist must be at least 6th level before selecting this discovery.
Wings is permanent, it is not activated by imbibing a mutagen. It allows only a limited number of minutes of fly in a day, and that is strange, as it is an Ex ability (they get tired?).
I checked but I haven't seen FAQs about those abilities.
Discoveries cover such a wide area that this is going to be a difficult thing to answer. As Diego Rossi pointed out some discoveries are permanent modifications to the character. Obviously, those are going to be always in effect
Discovery (Su): At 2nd level, and then again every 2 levels thereafter (up to 18th level), an alchemist makes an incredible alchemical discovery. Unless otherwise noted, an alchemist cannot select an individual discovery more than once. Some discoveries can only be made if the alchemist has met certain prerequisites first, such as uncovering other discoveries. Discoveries that modify bombs that are marked with an asterisk (*) do not stack. Only one such discovery can be applied to an individual bomb. The DC of any saving throw called for by a discovery is equal to 10 + 1/2 the alchemist's level + the alchemist's Intelligence modifier.
The description of the class ability Discovery does specify that Bomb discoveries do not always have to be used, and in fact only one at a time can be used on a particular bomb. That would imply that discoveries do not always have to be used. The real question is does that apply to mutagens? When an alchemist gains a discovery that alters mutagens is it the alchemist being changed or is it the mutagen that is altered?
A non-alchemist who drinks a mutagen must make a Fortitude save (DC 10 + 1/2 the alchemist's level + the alchemist's Intelligence modifier) or become nauseated for 1 hour—a non-alchemist can never gain the benefit of a mutagen, but an alchemist can gain the effects of another alchemist's mutagen if he drinks it. (Although if the other alchemist creates a different mutagen, the effects of the “stolen” mutagen immediately cease.) The effects of a mutagen do not stack. Whenever an alchemist drinks a mutagen, the effects of any previous mutagen immediately end.
Purging Mutagen (Healer's Handbook pg. 11): The alchemist’s mutagen combines ipecac and other purgative components. A non-alchemist who consumes the mutagen is nauseated for only 1 round, during which time her body rapidly metabolizes or expels all extant toxins, granting her an immediate second saving throw against each ongoing disease and poison currently affecting her. Each successful save counts as two consecutive successful saving throws for the purpose of curing the affliction. Any failed saving throws do not result in additional damage or other effects. A non-alchemist who consumes a second purging mutagen in a 24-hour period is instead nauseated for 1 hour. When an alchemist drinks the mutagen, he can choose whether or not to also be affected by this discovery in addition to the mutagen’s other effects.
To me the first bolded section indicates that the discovery is altering the mutagen instead of the alchemist. The second bolded section further reinforces the idea that it is the mutagen not the alchemist that is being altered. Purging Mutagen actually states the alchemist can choose whether or not to be affected by the discovery. Taking all of the above into consideration it would seem that unless the discovery is creating a permanent effect the alchemist can choose whether to use them.
As a final note it seems really silly that an alchemist would forget how to make a standard mutagen after leveling up. Why would an alchemist who is 1xp point away from leveling up not be able to create the same mutagen he created after killing a giant rat?
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So it may be a case by case basis you need to speak to each specific GM then. I was looking into it some more after sleep and I have seen people saying that mutagen abilities e.g. feral mutagen don't apply to cognatogen's. Quoting things like inspiring cognatogen that only applies to them and that most things like feral mutagen only sepcify mutagen. Which would have a large impact if you take true mutagen as the 20th level discovery if you play a game at that level. If cognatogen's are treated as mutagens you could have a feral cognatogen that grants +8 to all stats, if not you could have a mutagen that grants 8 to all physical stats and applies the feral modfiications or a cognatogen that grants +8, +6 and +4 to a mental stat only. quite a power difference. I had gotten the wrong idea about wings as I usually saw it posted in combination with feral. Hmm I'm also seeing a lot more mutagen altering abilities I didn't know of wonder if you can make a feral, fey one.
Thanks for the replies.
There is nothing that says multiple discoveries for mutagens don’t stack or limiting you to only using one. The only thing that is limited like that is bombs.
Cognatogens are not mutagens, so I don’t think the mutagen discoveries work on them. Nor would the cognatogen discoveries work on mutagens.