SPOILER!!! Only read this if you've completed the game.

Did anyone notice a change in Sam's eyes?

Her eye colour is brown, but In the end movie, when you see her in close up while she's saying "you've saved me, I knew you would" to Lara, you can see her eyes are sort of blueish grey.

Does that mean she has a little piece of Himiko inside of her?

What do you guys think?

Wow. Good observation there. I need to check it out!

Take a look at this video (for instance): http://youtu.be/G7v53Mft70U

and take a close look at Sam's close-up from 01.56-02.03.

It's an xbox-clip, but on the ps4 her eyes looked exactly like that.

Was hard for me to tell in that clip as it wasn't in HD. Could have been the after effects of the entity leaving her body together with the light that shined from above.

Still... would make an interesting concept if that was the case.

It's definitely not the light shining from above. Could've been an after effect, but it's really very clear to see (on a desktop-pc or bigger screen, but also on my phone).
P.S. You can choose HD from the settings menu at the bottom of the You Tube video screen ;-)

On the other hand, maybe Lara survived some encounters with Himiko with help from the current vessel? For example, when the wind carried away a huge samurai, but Lara remained. Or just deus ex machina?