The Hounds of the Baskervilles allusion/reference/whatever in the London Arc of the show. In Hounds of the Baskervilles, Watson is unaware that Holmes had actually been with him at the estate the entire time and is understandably upset when he finds out, as Ran is when she discovers Shinichi was at London with her.
Ran: I did so much research, and was worried to death about your stuff... Wasn't that stupid of me?
And Watson in Hounds of the baskervilles: ‘Then my reports have all been wasted!’ My voice trembled as I recalled the pains and the pride with which I had composed them.
I don't know if it was obvious to other people but when Shinichi was chasing Ran after the confrontation at the phone booth also in the London Arc, and he manages to grab her arm, it didn't occur to me that Ran is a karate expert and could have totally escaped from him by yanking her arm out one way or another, but when it did I realized... it was because she didn't want to. The one grabbing her was Shinichi, the guy she loves and she almost never sees, so she wants to stay with him no matter what.
File 131 or so: Yukiko manages to cover for Shinichi in front of Ran by saying Conan is really her distant relative, in fact, he's the nephew of the grandfather of the cousin of the daughter of the brother of her uncle. Follow it and realize that Yukiko is really saying that Conan is her son!
In the early days of the series, Conan would wear the bowtie suit thing all the time. I've never really thought of it since lots of cartoon characters wear the same thing every single day until rewatching the part where he says that his old primary school clothes is the only thing that fits him now. He had the outfit because he was turned into a kid and had nothing else to wear for a while.
Also note that Conan attends Teitan Elementary School, the same one as little Shinichi did, so as long as they didn't change the uniforms, he'd fit just fine.
Teitan Elementary School doesn't have a uniform. When he says "old primary school clothes" he just means clothes that he wore when he was primary school age. It's also fare to mention that in the early seasons, a lot of characters had Limited Wardrobe, not just Conan.
As noted on the main page under Call Back, the killer's room in "The Forgotten Bond" has a picture of Tatsuya Kimura from "The Karaoke Box Murder Case" on the wall. This isn't just an Easter Egg for observant viewers; both episodes are instances in which the Asshole Victim wasn't actually as much of a Jerkass as the killer believed. Nice Foreshadowing.
In the first case with the guy who killed himself with a knife in his back by leaping unto a knife from a chair. The knife was held by ice and it melted because blah blah blah... But why was he on his front when he was found!?
It was a very large block of ice with the knife attached, and the blade wasn't all-in his back although he died just fine, so I think it's enough for him to roll over a bit after he stabbed himself in the back
Conan has, several times, made deductions based on the idea that a certain action pertaining to the crime couldn't have been done by a woman, because a woman would not be physically strong enough to do it. He has spent his entire life as friends with a girl who can break stone, bend metal, and knock down doors with her fists, all without changing her facial expression. Yes, the idea that women are physically weaker than men is an example of Japanese Values Dissonance, but how do you argue that when one of the main characters is a woman stronger than many of the male ones?
In the moonlight sonata case, Conan says something like "I don't think the average woman could do that." remarking on how the murderer carried the body outside. So I guess Ran is just supposed to be an abnormality.
Data point: Ran's abnormality was recently lampshaded—unlike most women, her ring finger is longer than her index finger.
I believe Ran does all that through Karate, which is technique based, not strength based. Doing the things she does is different than having the raw power needed to carry a body.