These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Applicability: Particularly in the first game, as GLaDOS's dialogue provides most of the game's atmosphere and world-building. The creators have encouraged the vast numbers of Epileptic Trees about the series, and about GLaDOS' character in particular. It has provoked a lot of professional analysis and extrapolation about her meaning and symbolism. See for yourself.
Breather Level: After being shot at nearly every time you turn a corner and open a door in chamber 16 you immediately have chamber 17 where the worst thing you may encounter is easily dodgeable energy blasts. And maybe regret over having to "euthanize" the companion cube.
Cargo Ship: Chell/Companion Cube is a popular shipping pair in the fandom.
The Rat Man's graffiti shows he was far too attached to his Companion Cube, and really didn't take having to incinerate it at all well.
The Lab Rat comic proves that he failed to incinerate it, carrying it around with him and even talking to it (including hallicinations of responses) in his psychotic mania.
Ellen McLain talks about the experience of being GLaDOS (including a very sexy voice, an unexpected burst of opera singing, and a scary laugh). Have a listen to some commentary.
Cult Classic: Its popularity despite being a pack-in game for a Half-Life compilation owes itself to very good word of mouth from its fans.
Ear Worm: "Still Alive", the end song, is incredibly catchy. Which is pretty par for the course, as the song is written by the great Jonathan Coulton.
Ensemble Darkhorse: The Weighted Companion Cube. It was intended to be this to begin with in the game, but even Valve admitted they vastly underestimated the extent to which it was adopted as a fan favorite.
Everyone Is Jesus in Purgatory: There have been some truly odd interpretations of this fairly straightforward game as, among other things, a crushing feminist assault on the masculine and misogynist games industry. See the Wild Mass Guessing page for details.
Genius Bonus: Some people have deciphered the morse code tied to the new achievement. It appears to be GLaDOS rebooting.
GLaDoS being a killer AI. The trailers for the sequel don't try to hide this fact.
It's Short, so It Sucks : Gloriously averted, despite Portal lasting around 4 hours overall and lacking any real replayability. Portal being packaged into The Orange Box - and later sold separately as an Xbox Live Arcade game - was probably a big reason behind the lack of negative criticism for its brief length.
More Popular Spin-off: It's hard to remember that Portal, which technically takes place in the Half-Life universe, started off as a pet project ("a little lagniappe", in McLain's words) that was included as a bonus game as part of the compilation The Orange Box.
Sacred Cow: Like all of Valve's games, no one will let you off easy for disliking it.
Ships That Pass In The Night: Gordon Freeman and Chell is a popular ship due to their ridiculous number of similarities, despite the fact that, as far as we know, the two have never met, and are currently in completely different countries, possibly even in different time periods.
That One Level: The Advanced Test Chamber 18 will have you tearing pieces of yourself out in frustration.
Rather notably, Chamber 17 started out as one for the playtesters, as they had trouble adjusting to having to carry the cube around the whole time rather than leaving it behind after one use, and especially couldn't quite wrap their brains around using it as a shield in the opening corridors. The result was the Companion Cube.
The Tetris Effect: Not only the game-fun part, but you'll find yourself wishing you had an Aperture Science Handheld Portal Device for real-life transportation. And planning out the most efficient way to get from here to the fresh-produce aisle. Thinking With Portals, indeed!