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.
Broken Base: Some fans ran into a few problems with this over Gwen in the first two seasons. What really dug a divide between previously calm fans were the events of Children of Earth's Day Four and Day Five. Be careful about any criticisms OR compliments you have about Ianto's death or how it was handled.
Die for Our Ship: Gwen is perceived as getting in the way of Jack/Ianto, despite the fact that she married someone else.
Others view Ianto and, to a lesser extent, Rhys as getting in the way of Gwen/Jack.
Faux Symbolism: End of Days has this in spades. Abaddonnote A.K.A. The Devil is unleashed by Owen, Gwen, Ianto and Tosh opening the rift, going against Jack’s explicit orders not to. Jack ends up performing a Heroic Sacrifice to stop Abaddon, even dying in a Crucified Hero Shot. He remains dead for several days, then rises and immediately forgives those who betrayed him.
"Funny Aneurysm" Moment: Ianto's offhand comment that his dad was a master tailor in "Something Borrowed" leaves a different taste in your mouth after Children of Earth.
Ho Yay: Lampshaded by Jack in the episode "Meat", where he simply turns to Gwen and comments, "This is quite homoerotic."
Owen spends the first half of season one being pure Jerkass, with the woobie elements coming in later.
Though the Woobie elements have been hinted at since "Ghost Machine", where Owen is deeply affected by witnessing a young woman's brutal rape and murder from years ago. The machine did cause him to feel her emotions, but that doesn't change that Owen was deeply affected to the point of nearly killing her (now old and mentally unsound) murderer - yet when the old man was dying, Owen's instincts as a doctor kick in and he tries to unsuccessfully save his life.
Gray is either this or a Woobie, Destroyer of Worlds, given that the reason he's criminally insane and psychotic is because he was kidnapped and tortured as a child after his beloved older brother let go of his hand. This doesn't stop him from crossing the Moral Event Horizon later though, and even John Hart tells Jack that the chances of redeeming him after what he's seen and done are slim to none.
Rescued from the Scrappy Heap: The more we learned about him, the more likeable he became, especially after his death - not only did this mean he couldn't be a Loveable Sex Maniac/Really Gets Around sort anymore (though he'd grown out of it by now), it also enabled him to have more depth as a person in his following episodes, and when he's Killed Off for Real later it's utterly heartwrenching, even if part of this is because Toshiko went at the same time.
Owen going bananas over Diane after knowing her for all of a week.
The overly romantic light that Jack and his relationship with the real Jack Harkness was painted in might count too, as they only know each other for a couple of hours.
Ianto accused Captain Jack of being a monster after the Captain killed Ianto's Cyberman-girlfriend in defense (long story). However, Ianto goes back to shagging Jack by a few episodes with no significant on-screen development. Mellows somewhat in Season 3 when the two actually have more frequent conversations and develop a more emotional relationship.
Unfortunate Implications: Owen uses a cologne that gets people interested in him in the first episode. A high-tech date rape drug, in other words. Fridge Horror for some... And immediate horror for others. Has to be chalked up to first episode weirdness to have Owen be anything other than a villain.