Tomb Raider/WMG

Lara Croft is a Slayer.
...Just to break up the monotony.

Lara Croft was one of the people who owned the Witchblade.
Imagine that for a few seconds and you'll know why I made that guess.
 * I'm imagining...and I don't get it. Elaborate, perhaps?
 * Because she has really big feminine aspects?
 * There was a special comic series where Lara had a crossover with Witchblade.

Amanda is Natla

 * She found another time portal and used it to get to Avalon. However, thousands of years previously another portal was opened in ancient Atlantis. Amanda inadvertantly travelled back to this point and the Atlanteans declared the mysterious future woman to be their ruler. They had her DNA mixed with Atlantean DNA, so she could gain their powers (immortality, wings, etc.) but still retain her (slightly modified) human appearance. Amanda took the name Natla from the weird crates she'd seen lying around...
 * And then, upon returning to the present as Natla, had the crates put there so that her past self would see them and take her name from them. How's that for a Stable Time Loop?
 * Well, Nata was only one of three rulers of Atlantis - Tihocan and Qualopec were the others.
 * Megajossed by Underworld.

Sofia Leigh will return

 * She's apparently indestructible. Lara kills her with electrocution in TRIII, then again with the radioactive meteorite in The Lost Artefact. However, theres no indication that she actually died the second time (we get the same pyrotechnic display on both 'deaths'). Quite likely she's out there somewhere, horribly mutated by the slime and unable to die, with her only wish to exact revenge on Lara...

The main portal to Avalon is in Atlantis

 * The biggest change that Anniversary made to the plot of the original game was the introduction of a backstory about Lara's father searching for the Scion, we also know from Legend that he always believed his wife was alive and was searching for Avalon. It's hard to imagine that the search for the Scion came first (Lara was nine when her mother "died", but she was old enough to help her father look for the Scion) so perhaps he had reason to believe that the Scion would help him in his quest. And of course, the return of Natla suggests that we haven't seen the end of the Atlantis plot.
 * Underworld has Natla but no Atlantis. Jossed.
 * Why do you say that? Clearly the presence of a winged, fireball-throwing Atlantean demigod would imply the existence of said former kingdom?

Lara really did die at the end of Last Revelation.
First, let's say the events of Legend, Underworld and the Xbox Live DLC take place directly after Tomb Raider III. At the end of Lara's Shadow, After this, Last Revelation and Chronicles take place, but Lara's body is never found. In honour of her likeness, the Doppelhoe goes off on her own adventure, also known as...Angel of Darkness. This explains Lara's "hardcore" personality in the game, and it's been established that the Hoe's appearance is based on Ao D Lara.

SPOILERS!
From Tomb Raider: Legend, the two sides of the conversation through the portal edited together: http://www.youtube.com/watch?v=qiFlkeNlFtE

The whole thing started when young Lara messed with the sword in the dais in Nepal, after the plane crash. They've miraculously survived a plane crash in the mountains, but surviving the night will be just as tough. Listen to Amelia, "Lara, have you found anything for the fire?" That's a mother putting on a brave face for her child, holding tight to the necessities of survival. Lara repays her care and worry by making more trouble, ultimately causing her mother to vanish.

Again, observe Amelia. "No, get back!" while quickly and instinctively moving her daughter away from this new unknown danger. Then young Lara's "There's something in the light," causes her mother to move back into danger, while ordering "Stay here." The future Lara speaks, "It's Lara, your daughter."

In Amelia's current state of mind this is a powerful trigger phrase. Facing a terrifying unknown she turns to look at young Lara while asking "What about my daughter?", then a plaintive "You stay away from her. She meant no harm."

Then Amanda, despite being abandoned by Lara to drown; despite Lara's bull in a china shop approach that led to the death of Rutland, her benefactor; despite her defeat at Lara's hands in unnecessary combat, Amanda still tries to help.

Even now if Lara had listed to Amanda's advice all would have been well. Her half-hearted attempt to pull out the sword turns into a cowardly retreat, sealing her responsibility for her mother's fate.

Lara suffers a psychotic break, screaming and shooting, but not to kill, not even to wound. She does finally lash out physically, "From now on your every breath is a gift from me," is a reflection of Lara's realization that's a gift she stole from her own mother.

From now on she'll consciously blame anyone but herself for Amelia's doom, but she knows who's responsible. Older Lara puts a brave face on it.

Younger Lara notes carefully the configuration of the stones, leaving behind the drawings of the Yeti along with her childhood. Lara's "This is what it's always been about" is oh so true.

But not half as true as, "Amanda said you were sloppy."

When Lara meets her mother in Underworld she goes into full denial, shouting whiny self-justification for having to finally deal with the mess she's made of her life, her father's life, and most horrifyingly, her mother's life.

At the end of Underworld Lara no longer cares what Amanda does, "Would killing me make us even?" as she sheathes the weapon that had defeated Amanda before. Perhaps she's hopeful that Amanda will take her burdens from her. What's Lara to do with her life-long motivation not only gone, but an abject failure?

Then she picks up her childhood drawings of the Yeti. She's returning to her childish fantasies in an attempt to escape from the reality of her guilt.

At the end Lara's Shadow she goes even farther in projecting her guilt. Instead of just blaming Amanda, she turns to pointlessly torturing others.

- JoveHack

Natla is still alive.

 * I think Natla is still alive but trapped in that pool until the end of time.

The ammunition, medical packs, weapons Lara found...
...They are what previous explorers left when they died. Most of the supplies are found near animals because the animals killed them and ate them, which is why there are no remains. Lara is much more able than most explorers so she survives.

The Crystal Dynamics trilogy takes place in the same universe as Assassin's Creed.
An argument could be made for the whole series, but the newer games really fit the hypothesis to a tee, since we're only given a vague Ancient Astronauts implication for the origins of such advanced tech. Atlantis could have very easily been a First Civilization settlement. Natla's one of the Ones Who Came Before, and she's aligned herself with the Templars for her own ends, with Natla Industries serving as another front business like Abstergo. The Scion, Mjolnir, and similar artifacts are all Pieces of Eden, or remnants of First Civilization tech. Assassin's Creed II mentions Vaults all over the world, and the "underworld" temples like Helheim, etc. correspond to some of those. Lara's father could well have been an Assassin himself, or similar to Tesla, ran to help the Assassins retrieve artifacts after being targeted by the Templars once he turned on Natla. Zip and Alister could even be Rescued from the Scrappy Heap in such a scenario, as an Assassin support team similar to Shawn and Rebecca, secretly sent to help Lara in her treasure hunting to keep the artifacts away from the Templars.

The Philosopher's Stone is a fragment of the Hand of Midas from the first game
No explanation really needed, they both have very similar effects.

Lara is part of the Wold Newton family
It'd make a lot of sense.