Here is part two of a list of my favorite episodes of the modern series of Doctor Who (which begins in 2005). I call the series numbers "seasons" because I'm American, in case that causes any confusion. Spoilers, of course.

Season 6 Episode 1: The Impossible Astronaut
Season 6 Episode 2: Day of the Moon

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In this two-parter, Amy, Rory, & River are sent to Utah by The Doctor, who gets shot by an unknown astronaut. They're then sent to Washington D.C. in 1969, where they meet President Richard Nixon. They encounter an alien race called The Silence who make people forget them as soon as they look away.
"I am being extremely clever up here and there's no one to stand around looking impressed. What's the point in having you all?"

Season 6 Episode 4: The Doctor's Wife

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The Doctor gets a distress signal from a junkyard on an asteroid outside of our universe called "House". The "soul" of the Tardis is transferred into a real woman. With plans to steal The Doctor's Time Lord energy, the controller of House possesses the Tardis, trapping Rory and Amy inside.
"Are all people like this?"
"Like what?"
"So much bigger on the inside."

Season 6 Episode 7: A Good Man Goes to War

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"Amy" has been an avatar made from shapeshifting material called "The Flesh". The real Amy was abducted and taken to an asteroid base called "Demons Run", where she has given birth. The Doctor and Rory gather allies and form an army to attack the base and save Amy and the baby.
"Demons run when a good man goes to war. Night will fall and drown the sun when a good man goes to war. Friendship dies and true love lies. Night will fall and the dark will rise when a good man goes to war. Demons run, but count the cost; the battle's won, but the child is lost when a good man goes to war"

Season 6 Episode 10: The Girl Who Waited

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The Doctor takes Amy & Rory to the planet Apalapucia, not knowing it's under quarantine due to a deadly plague that threatens the two-hearted inhabitants. Amy is separated from the group, and when The Doctor and Rory come to save her, they find they've arrived 36 years later in her timeline.
"I'm gonna pull time apart for you."

Season 7 Episode 2: Dinosaurs On A Spaceship

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The Doctor gets a call to a vast spaceship in 2367 that if not destroyed by missiles, will crash into Earth in 6 hours. He assembles a team--including Queen Nefertiti--that encounter dinosaurs, sassy robots, and a man named Solomon who murdered the ship's inhabitants.
"This is a two-man job! And what are you doing?"
"I'm easily worth two men. But you can help if you like."

Season 7 Episode 4: The Power of Three

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Mysterious black cubes appear all over Earth and The Doctor stays with Rory and Amy to investigate. He encounters the alien Shakri, who want to destroy humanity, which they believe to be an infestation.
"I'm not running away from things. I'm running to them, before they flare and fade forever."

Season 7, 50th Anniversary Special: The Day of the Doctor

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On the last day of the Time War between the Daleks & the Time Lords, the unknown War Doctor decides to destroy Gallifrey to end the war. This parallels a present-day decision by UNIT to destroy London rather than allow the alien race of Zygons to invade.
"You know the sound the Tardis makes? That wheezing, groaning? That sound brings hope wherever it goes. To anyone who hears it, Doctor. Anyone, however lost. Even you."

Season 8 Episode 7: Kill the Moon

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The Doctor takes Clara & her student Courtney aboard a space shuttle in 2049. The shuttle & its crew are on a suicide mission to destroy Earth's moon, as years ago it caused massive high tides on Earth that killed many people. Surviving the crash landing, they encounter a dead Mexican lunar colony and an abyss filled with massive spider-like creatures.
"Tell me what you knew, Doctor, or I'll smack you so hard you'll regenerate."

Season 9 Episode 11: Heaven Sent

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The Doctor is teleported to an ever-shifting and resetting castle that's surrounded by water. While being pursued by a murderous cloaked creature called "The Veil", he discovers that the castle is a trap designed to extract confessions from him.
"It's funny. The day you lose someone isn't the worst; at least you've got something to do. It's all the days they stay dead."

Thanks for reading! Check out Part 1 if you'd like.