Warning Only read this if you have beaten Portal and Portal 2 single player as this contains the biggest spoiler of them all.

After playing and beating both games and reading the comic i have figured it out:
Spoiler 1(which some people have already posted)
GLaDOS is Caroline

Spoiler 2(which no one has posted)
Caroline is Chell’s Mother

Spoiler 3(from what I can tell which no one has figured out yet)
Chell is Cave’s and Caroline’s Daughter!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Update: Possibly Adopted by another employee to hide the birth of Chell from Cave.

Evidence Spoilers
Picture one: Cave and his Wife Caroline(aka GLaDOS – who also adds that the people in the pic look familiar) http://goo.gl/afxC1

Proof in the olden days oil self portraits didn’t include anyone else unless it was a wife or family member – wikipedia http://goo.gl/rkVBM

After people started enhancing the portrait I too did the same:
http://goo.gl/yRtps

It appears to be a female the size of a child on the left side of it and the reason the picture would of been done like this is that Cave didn’t want a child and so he would of neglected her thus putting her in the picture would of probably been Caroline’s idea and may have been added after the main picture was painted thus creating the see threw-ish effect; That Or the female embedded in the dark part of the portrait is part of the deep embedded Greek Mythology the game is based on and keeps referring to.

So I was playing the reunion chapter again and I found another picture in a different room from the other one of Cave and Caroline then boom I got this “Portrait of a Lady
Find a hidden portrait – Unlocked: Apr 23, 2011 1:08am” And GLaDOS Also comments on it!

Picture two: pic 1 Cell’s science project from Bring your child to work day science fair http://goo.gl/N5Bxc
Picture three: pic 2 Cell’s science project from Bring your child to work day science fair. http://goo.gl/DV9iz

Update2: I’m still surprised no one has gotten this so I guess I’ll say it. Chell’s project is of a growth acceleration with the use of some “Stuff”(possibly some chemical they used to mature clones or moon dust or both) that she got from her Father(cave) from his work for the project; So This could also explain Chell’s age when she woke from cryo in the first portal and why the chamber looks like it was an egg(because the cryo chamber was an growth accelerator incubator).

Here http://goo.gl/xGggl in the comic you see a teddy Bear besides Chell’s 1st cryo chamber/incubator!

Here http://goo.gl/RNGGN you see Chell’s file as she is a child and lastly here http://goo.gl/sfuHm after the events of portal 1 you see her file as she is an adult.

The translated Opera turret song (Used Google translater)

Cara, bel, cara mia, (Dear, beautiful, my dear,)
bella bambina, (beautiful child(girl),)
oh Chell, (Chell oh,)
que lastima, (that’s too bad,)
que lastima, (that’s too bad,)
deh! Cara mia, (well, My dear,)
addio. (Goodbye)

Mia bambina, ( My Baby)
cara, (dear,)
perchè non passi (why don’t you stay(run))
lontana, deh ( far, ah)
sì lontana ( so far)
da scienza? (from science?)

Cara, cara (Baby, baby)
mia bambina, (my child(girl),)
ah mia bel, (ah my beautiful,)
ah mia cara, ( ah my dear,)
la mia cara, (my dear,)
la mia bamina, (my child(girl),)
oh cara, (my dear,)
cara mia… (my dear…)

Full song in place:

“Dear, beautiful, my dear”
“beautiful child(girl)”
“Chell oh”
“that’s too bad”
“that’s too bad”
“well, My dear”
“Good bye”
“My Baby”
“dear”
“why don’t you stay(run)”
“far so far”
“away from science?”
“Baby, baby”
“my child(girl)”
“ah my beautiful”
“ah my dear”
“my dear”
“my child(girl),”
“my dear”
“my dear…”

Original Source: http://goo.gl/pMkMn

Also In the final song GLaDOS mentions about her daughter on lines 12-14 and 31 which:

“Well here we are again”
“It’s always such a pleasure”
“Remember when you tried to kill me twice?”
“Oh how we laughed and laughed”
“Except I wasn’t laughing”
“Under the circumstances”
“I’ve been shockingly nice”
“You want your freedom? Take it”
“That’s what I’m counting on”
“I used to want you dead but”
“Now I only want you gone”
“She was a lot like you”
“Maybe not quite as heavy”
“Now little Caroline is in here too”
“One day they woke me up”
“So I could live forever”
“It’s such a shame the same will never happen to you”
“You’ve got your short sad life left”
“That’s what I’m counting on”
“I’ll let you get right to it”
“Now I only want you gone”
“Goodbye my only friend”
“Oh, did you think I meant you?”
“That would be funny if it weren’t so sad”
“Well you have been replaced”
“I don’t need anyone now”
“When I delete you maybe”
“I’ll stop feeling so bad”
“Go make some new disaster”
“That’s what I’m counting on”
“You’re someone else’s problem”
“Now I only want you gone”
“Now I only want you gone”
“Now I only want you gone”
“Now I only want you gone”

Chell’s age, rapid aging(aka Stasis) and lastname read here http://goo.gl/xBmcy

Look at the similarities http://goo.gl/zxX5a

Also Chell’s eyes are white/silver like the color of the moon and that could be dew to her father cave testing moon dust on himself; Proof and I quote from the game “Cave Johnson: The bean counters told me we literally could not afford to buy seven dollars worth of moon rocks, much less seventy million. Bought ‘em anyway. Ground ‘em up, mixed em into a gel.” – “Cave Johnson: And guess what? Ground up moon rocks are pure poison. I am deathly ill.” – “Cave Johnson: That said, I would really appreciate it if you could test as fast as possible. Caroline, please bring me more pain pills.”

_{* I gathered some of these notes from other sources on the web and combined them here}