The description of the synthesist summoner's fused eidolon says, "Neither the synthesist nor his eidolon can be targeted separately, as they are fused into one creature." Do effects that buff allies, grant allies special abilities, or deal damage affect both the summoner and the eidolon if the effect isn't targeted? For example, does a fireball deal damage to both the synthesist and his fused eidolon?
No, they are a single creature (with exceptions)
Whenever you and your eidolon meld into each other, you both cease to exist as individual creatures, you simply act as one and are affected as one. Your eidolon still has his hp pool and you have your own, but as one being you add his hp as temporary hp to yourself.
Neither the synthesist nor his eidolon can be targeted separately, as they are fused into one creature.
Nothing can target your eidolon or your character anymore as individual targets, regardless if it's an area effect or not. Unless an exception exists (see bellow).
There is also a FAQ item about this topic:
Summoner: What happens when a synthesist (page 80) takes a penalty, suffers an affliction, or has an ongoing effect when the eidolon disappears?
These effects persist on the summoner after the eidolon is gone. For example, a ray of enfeeblement on the fused character continues to affect the summoner after the eidolon is gone, as would a bestow curse spell or acid arrow spell, as would continuing poison damage. These effects apply to the character as a whole, and just because the eidolon is gone doesn't mean the summoner is freed from the effect (ability damage is tracked separately, as described in another FAQ, because it is a separate game statistic that the summoner "borrows" from the eidolon). If the condition or effect ends (whether from its duration running out, being cured/negated/dispelled, and so on) while the eidolon is gone, it doesn't return when the eidolon is resummoned. This applies to beneficial effects as well as harmful ones--an invisible summoner isn't suddenly visible if his eidolon disappears, nor does he become invisible again if the duration ran out while the eidolon was gone.
Your eidolon can still be killed while fused with you.
The synthesist gains the eidolon’s hit points as temporary hit points. When these hit points reach 0, the eidolon is killed and sent back to its home plane.
To prevent this, you can use your Life Link ability to sacrifice your own hp to prevent damage on your eidolon. And you can still target your eidolon with Rejuvenate Eidolon, even if normally he can no longer be targeted by spells. The spell Life Conduit does not target your eidolon (it's Personal) and allows you to share hit points between each other.
And lastly, even if you gain his hp as temporary hp, you should still track his hp separatedly from your other temporary hit points, so you don't get them mixed up.