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As I see it, there are two eras of My Little Pony: Friendship is Magic, the first one within Seasons 1-4, and the second from Season 5 onwards. A lot of the episodes appear to have a lot of similarities between the two different eras. Here's what I think they are:

First era (Seasons 1-4) Second era (Seasons 5+) How similar?
Friendship is Magic - parts 1 and 2 The Cutie Re-Mark - parts 1 and 2 Both are episodes where Twilight makes friends with new ponies.
Griffon the Brush Off The Lost Treasure of Griffonstone Both feature Gilda.
Boast Busters No Second Prances In both episodes, Trixie puts on a magic show.
Dragonshy Scare Master Both are Fluttershy episodes that the Mane Six also play a big role in.
Look Before You Sleep Applejack's "Day" Off Both are Applejack/Rarity episodes where they relax in a certain location.
Bridle Gossip Slice of Life Both are episode #9's that Zecora appears in.
Fall Weather Friends Buckball Season Both are episodes about sports.
Suited For Success Canterlot Boutique Both are episode #14's that focus on Rarity.
Sonic Rainboom Rarity Investigates! Both are Rainbow Dash/Rarity episodes.
The Show Stoppers Crusaders of the Lost Mark Both are episode #18's that focus on the Cutie Mark Crusaders.
Green Isn't Your Color Fluttershy Leans In Both are Fluttershy episodes that I suspect will have a lot of similarities.
A Bird in the Hoof The Hooffields and McColts Both are Twilight/Fluttershy episodes.
Party of One Party Pooped Both are Pinkie Pie episodes with the word "party" in the title.
The Return of Harmony - parts 1 and 2 The Cutie Map - parts 1 and 2 Both two-parters focus on all the Mane Six.
Lesson Zero Every Little Thing She Does Both are episodes where Twilight and Starlight respectively struggle with friendship problems.
Luna Eclipsed Do Princesses Dream of Magic Sheep? Both are Princess Luna episodes.
Sisterhooves Social Forever Filly Both are Rarity/Sweetie Belle episodes.
The Cutie Pox Bloom & Gloom Both focus on Apple Bloom having a big problem.
May the Best Pet Win! Tanks for the Memories Both focus on Rainbow Dash and her pet Tank.
The Mysterious Mare Do Well 28 Pranks Later Both are Rainbow Dash episodes that feature a dark theme. (Thanks to RiceWaffleFox for this)
Sweet and Elite Spice Up Your Life Both are episodes where at least Pinkie Pie and Rarity visit Canterlot.
Secret of My Excess Princess Spike Both are episode #10's that focus on Spike.
Hearth's Warming Eve A Hearth's Warming Tail Both episodes are Hearth's Warming themed.
Baby Cakes A Flurry of Emotions Both episodes involve taking care of baby foals.
The Last Roundup The Mane Attraction Both are Applejack episodes where Pinkie Pie makes a semi-major role.
Hearts and Hooves Day Hard to Say Anything Both are Cutie Mark Crusaders episodes that feature Big McIntosh.
It's About Time Amending Fences Both are episodes where Twilight, Spike and Pinkie are in Canterlot.
Dragon Quest Gauntlet of Fire/Triple Threat Spike episodes that feature a group of big dragons.
Hurricane Fluttershy Flutter Brutter Both are Fluttershy episodes where Rainbow Dash has a semi-major role in.
Ponyville Confidential Appleoosa's Most Wanted Both feature the Cutie Mark Crusaders.
MMMystery on the Friendship Express The One Where Pinkie Pie Knows/P.P.O.V. (Pony Point of View) Episodes where hard puzzles are solved, often involving Pinkie Pie.
A Canterlot Wedding - parts 1 and 2 To Where and Back Again - parts 1 and 2 Both are two-parters where Queen Chrysalis is the main villain.
The Crystal Empire - parts 1 and 2 The Crystalling - parts 1 and 2 Both are two-parters that take place in the Crystal Empire.
One Bad Apple On Your Marks Both are episode #4's that focus on the Cutie Mark Crusaders.
Sleepless in Ponyville The Cart Before the Ponies Both are episodes where we only see the Cutie Mark Crusaders, Rainbow Dash, Rarity, and Applejack.
Wonderbolts Academy Newbie Dash/Parental Glideance Rainbow Dash episodes featuring the Wonderbolts.
Apple Family Reunion The Perfect Pear Both are episodes that involve Applejack's family members.
Keep Calm and Flutter On Make New Friends but Keep Discord/Discordant Harmony Discord/Fluttershy episodes.
Magical Mystery Cure A Royal Problem Both are episodes where cutie marks get switched around.
Princess Twilight Sparkle - parts 1 and part 2 Celestial Advice and All Bottled Up Both are episodes where a pony moves on with her life.
Castle Mane-ia Castle Sweet Castle Both are episode #3's and have the word "castle" in the title.
Daring Don't Stranger Than Fan Fiction Both are episodes where Rainbow Dash goes on a Daring Do adventure.
Power Ponies Dungeons & Discords Both are episodes where Spike goes on an adventure either with the Mane Six or two other friends.
Bats! Viva Las Pegasus Both are Applejack/Fluttershy episodes.
Rarity Takes Manehattan The Saddle Row Review Both are Rarity episodes that take place in Manehattan.
Pinkie Apple Pie Hearthbreakers Both are Pinkie Pie/Applejack episodes.
Three's A Crowd What About Discord? Both are Twilight episodes that feature Discord.
Simple Ways Made in Manehattan/Honest Apple Applejack/Rarity episodes.
Twilight Time The Fault in Our Cutie Marks Both are episodes that feature Twilight and the Cutie Mark Crusaders.
Somepony to Watch Over Me Brotherhooves Social Both are episode #17's that focus on Apple Bloom and another Apple sibling.
Maud Pie The Gift of the Maud Pie/Rock Solid Friendship Maud Pie episodes.
Leap of Faith Where the Apple Lies Both are Apple family episodes (I couldn't decide exactly which one fits the best).
Testing Testing 1, 2, 3 Top Bolt Both are Twilight/Rainbow episodes.
Equestria Games The Times They Are A Changeling Both are episodes that focus on Spike and are located in the Crystal Empire.

Note: A few episodes (so far, 6 out of 13 from Seasons 1-4) have similarities with two other episodes (from Seasons 5+). These episodes have no similarities yet:

From Season 7:

If you spot any similarities for the episodes above, let me know.