There is no reason to believe that alter self doesn't make the altered creature smell like, just as much as look like, the creature he is emulating. If you alter to an elf, you would smell like an elf.
If there was some reason to believe the subject creature had a particularly unique odor, such as always bathed in lavender or ate a lot of garlic, I might would give a circumstance bonus to a creature with sent to penetrate the disguise, but in general scent doesn't help this roll.
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On the other hand, if you used Alter Self to take the form of a Troglodyte, you would not get the stench aura of a troglodyte. I'd be willing to give a creature with scent a +10 to the perception roll to penetrate a disguise, offsetting the magical bonus from the spell.
Wolverine was able to detect Mystique via scent after all.
I just ran into this, and I pretty much ruled it exactly as your question implies.
Alter Self the spell magically changes you, so Dave's response is a good one: Unless you wear the same clothing or the same cologne, you'll smell different. I'd strongly argue that if you use Alter Self and then put on all your own gear, anyone with Scent is going to know you smell like one person and your gear smells like someone else's.
For shapeshifters like doppelgangers, it seems more like they're morphing themselves than magically altering themselves, so I'm more in Imbicatus' camp.
So you intentionally phrased it as two questions: A doppelganger and a wizard.
For the doppelganger, Scent works. For the wizard, as long as he/she has half a brain and changes outfits, it doesn't.
Basically a big old, "I'm interpreting the rules the way I feel like it, because it isn't explicit one way or the other and it just feels better this way..."
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"I'm interpreting the rules the way I feel like it, because it isn't explicit one way or the other and it just feels better this way..."
Which, while unsatisfying, is probably the most practical way to handle this and similar matters.
OK, a thought here. A creature without the enhanced olfactory abilities that the Scent ability provides may not be aware of the complexities and nuances that a creature with Scent would find obvious. Since the spell requires an actual bit of that creature type to cast, it is easy to posit that this will include scent as part of the polymorph "template". Hopefully your bit of flesh isn't from an oddball exemplar of the species.
If you rule that Eschew Materials removes the need for a bit of flesh, then fooling a foe with Scent becomes more of an issue. This would go with any sense that the caster doesn't possess.
The more I think on this, I would want to rule that the bit of flesh is a required focus and not a material component. The views of this do not necessarily reflect the views of this station.
EDIT/ADD
Didn't doppelgängers used to have to touch you to copy you perfectly (or thereabouts)? That would be the equivalent of the spell's bit of flesh.