I have a simple question-
If someone sees through a disguise created by magic, does that person know who the disguised person is, or just that it's a disguise?
"Hey doc, will I be able to play the piano after this operation?" "Depends. Can you play the piano now?"
The basic rule is that if you see through a illusion, it looks like a translucent image but you can see the truth underneath it. I would rule that if you see through an illustory disguise, you see what the person actually looks like. This doesn't mean, of course, that you know who it is. There are lots of undisguised people out there that I can see but not recognize.
I'd have to think about transformation-type disguises such as polymorph. Knowing that this is something-transformed-into-a-penguin doesn't mean that you know what that something is.
Alright then.
Change the question to alter self.
It's more of a question of "can i accomplish this"
Then the specific spell-
There is a character i have in mind that wants to remain anonymous.
Shrug. Put on a mundane disguise and then cast your disguise self spell. When they see through the spell, they'll see someone in a false beard and Groucho Marx glasses.
Oh, heck, go all the way and put on an Islamic niqaab. With a false beard on the outside.
Ok, that's hilarious.
Another thing that would work is a purple mask with "nope" written on the forehead.
Alter self, being a transmutation, can't be seen through without magical means, such as true seeing.
Beating the disguise check DC just means you know something is up, that it's not a real [whatever].
Orfamay Quest is dead on with disguise self/illusions though.
Don't forget that the character making the save must interact with (ie touch) you in order to get a save at all.