Austin Powers/WMG

Vanessa Kensington was a fembot sleeper agent who was unaware of her true nature.
Sometime before the bulk of the first film, the real Vanessa was replaced by a robotic duplicate who had been programmed with the memories and personality of the original. The sleeper fembot was unaware of her true nature, and she genuinely fell for Austin. It was only after the marriage that her assassination programming was triggered and overrode her Vanessa persona.

This explains how Vanessa can have a mother: there was once a real Vanessa. It also explains why she didn't take advantage of earlier opportunities to get rid of Austin.

Vanessa was replaced by a fembot immediately before the climax of International Man of Mystery.
She gets captured by Doctor Evil Alotta Fagina shortly before the climax. This is when the switch happens. The real Vanessa is still out there somewhere and will no doubt come bursting into the room at the end of the next Austin Powers movie and reveal the whole story to him and whoever his current Bond Austin Girl is.
 * Alternately, she was killed when she was replaced.

Mini Me is the test tube baby that Scott was supposed to be
We know that Frau lied, and that Scott is the natural son of her and Doctor Evil. Maybe they DID use Doctor Evil's sperm to clone him...and Mini Me is the result. (There is no disputing that Mini Me is a clone of some sort!)

The Austin Powers series is FAR from done
The following movies will be made:

Doctor Yeah, Baby! (Dr. No)

From the 60s With Love (From Russia With Love)

Thunderballs (Thunderball)

You Only Shag Twice (You Only Live Twice)

On Her Majesty's Secret Cervix (On Her Majesty's Secret Service)

Live and Let Shag (Live and Let Die)

The Man With the Golden Member (The Man With the Golden Gun)

Sequels Are Forever (Diamonds Are Forever)

Moonrakish (Moonraker)

For Your Ass Arse Only (For Your Eyes Only)

A View to a Shag (A View to A Kill)

The Shagging Daylights (The Living Daylights)

Licence to Shag (Licence to Kill)

Tomorrow Never Shags (Tomorrow Never Dies)

All the Babes in the World are not Enough (The World Is Not Enough)

Shag Another Day (Die Another Day)

Casino RoYeah, Baby (Casino Royale)

Quantum of Sol-Ass (Quantum of Solace)

Never Say Member Again (Never Say Never Again)
 * Somewhere, a porno namer is laughing with glee at this page.

There is a Judo-Christian God, and Austin Powers is his Prophet.
Inspired by an oft-forgotten "e" and the Rule of Cool.

Felicity Shagwell fell in love with Austin From Ten Minutes Ago.
This explains her absence in Goldmember and allows her to be more than just a Girl of the Week.

Felicity Shagwell settled down with the real Austin.
The Austin in Goldmember is Austin From Ten Minutes Ago.

The Austin from every movie onward will be a different paradox clone, and end up mated with his Bond Girl for life.
Thus subverting the whole point of the Bond Girl trope. When and if Vanessa returns, there's either going to be one of him free, or every one of him is going to be in a lot of trouble.

The first movie takes place over the course of a year.
The first one takes place in 1997, but at the beginning of the second movie, it's 1999. In the second movie, it says that Austin was frozen in November 1967 and was unfrozen thirty years later, so the movie could take place in November 1997 once he's unfrozen. It's possible that the mission to infiltrate Verticon ended sometime in late 1998, with time skips that aren't indicated or mentioned in the film. Vanessa holds a grudge against Austin for sleeping with Alotta Fagina for a period of months. Austin and Vanessa then get married then in early 1999.
 * But doesn't this all take place within the week (I think it was) that Dr. Evil gave the UN to pay him the 100 billion dollars?

Real Vanessa got swapped with fembot Vanessa in between the first two films.
Nobody's seen her since. Yeah, this is just an excuse for the real Vanessa to survive.

Dr. Evil is a cronic nail biter
He is alwyas trying to remove a phantom nail, it's been gone since his dad left him but, he misses his dad so much he doesn't beleive it's trully gone.