I'll be upfront here: Making a good humanoid SCP object is tricky business. It's easy to empathise with a humanoid. They have a face, and usually feelings. Some of them even have personalities. It's really easy to forget to be clinical when describing them. They're overwhelmingly more likely to be a Mary Sue than any other SCP type. Because of all this, when you make one, people are going to be putting it under much heavier scrutiny than a non-humanoid SCP object would be, and the standards are more stringent.
The single most important piece of advice I can give you is this: Do not write about your humanoid SCP object as if it is a person. Notice how I used the term "humanoid SCP object" there. There's a reason for that. An SCP that breaks any one of the other rules in this article can still be potentially made to work anyway if this one is followed strongly enough. If you want to see a great example of this, SCP-890 is your guy(-shaped thing).
That's not to say that the SCP object itself has to be completely devoid of personality or feelings, or that it shouldn't be afforded a modicum of basic human decency if it's sufficiently non-malicious (the Foundation isn't unnecessarily cruel, after all), but your SCP article is a piece of executive documentation on an SCP object. If you're going to paint your humanoid SCP object as something worthy of compassion, highlight it by your article's coldly pragmatic lack of compassion. At most, you might be able to get away with writing about it as if it were an animal and you its zookeeper, assuming that it's not very dangerous. Note that I'm using the term "it" instead of "he" or "she" or "they"; I very strongly recommend that you follow suit. (Exception: SCP-029 gets away with using gendered pronouns because she is completely unsympathetic.)
As an extension of this, since your humanoid SCP object is not a person, it should always be referred to by its official designation in official documents, rather than any name or other appellation that it prefers, because what it prefers to be called does not matter. In some circumstances, it may be appropriate for staff directly speaking to the SCP to address it by its preferred name (e.g. SCP-811 has a poor grasp of language, so using the name it already recognises as its own greatly streamlines communication), but "it gets moody/angry when called a number" is generally not a good reason for this. Also try to come up with a descriptor rather than a nickname for their mainlist "title" (e.g. something like Abdominal Planet, Star-Eyed Child, as opposed to something like "Vector").
The second big thing to consider when making a humanoid SCP object is avoiding "X-men Syndrome". As a rule of thumb, if what's anomalous about your humanoid SCP object can be most accurately described as a voluntary "power" or "ability", you should probably start over. Slapping on some superficially nasty drawbacks, making them ugly, and/or giving them an awful personality won't fix it, either. To quote a wise and frequently abrasive man I know and in some cases admire1:
Let me tell you a story.
A rich man once went to visit the home of a poor relative who lived in a ghetto. He wore his best suit, because when you make a social call, it's polite to dress up, right? As he was walking to the house, he was attacked and robbed, because he looked like he had money.
The next time he visited, he also wore his best suit, but this time he rubbed mud into the lapels and tore a seam so it looked a bit rougher. To his surprise, he was mugged again, because even though he looked a bit worse for wear he still looked offensively better off than everyone else.
Trying to disguise something extraordinary by making it superficially ugly, unlucky, painful, or whatever just doesn't work. Frankly, it's appallingly poor writing technique. If you write a character with a magic power, no matter how unfortunate you make them they're still a magical person.
Or, to paraphrase, an X-man who's a jackass, disabled, and lets loose a horrifically stinky fart every time he uses his powers is still an X-man. (Exception: SCP-353 tried to be a Marvel Comics style villain, and the Foundation brutally smacked that down with amnestics and harsh containment procedures) That's not to say that your humanoid SCP object's anomalous effects shouldn't have drawbacks; quite the contrary, a huge part of making many humanoid SCP objects work is giving the readers the feeling of "Sweet [insert deity or deities of choice here], I'm glad I'm not that guy."
There are two words in the paragraph describing the second rule that are more important than the others.
The first is "voluntary". The thing that usually makes or breaks a case of X-Men Syndrome is whether or not the anomalous effect in question is voluntary on the part of the SCP object or not. SCP-590's effect, for instance, happens any time it touches another human being regardless of its will, and the Foundation exploits that fact ruthlessly. Mr. Deeds, while incredibly powerful in the sheer broadness of its capabilities, has no real will of its own and can only use those capabilities at the behest of whomever rings its bell. SCP-027-2 is much more the victim of its anomalous effects than the master, as are SCP-273, SCP-817, and SCP-507, the last of which will be talked about in more depth later.
The second is "superficially". Any nasty drawback or adverse circumstance you decide to inflict on your humanoid SCP object should actually be substantially detrimental to them, and preferably in a way that logically follows from their circumstances, rather than it being just tacked on for balance. It's similar in principle to why you shouldn't give story characters cop-out flaws like "too nice" or "clumsy" unless you're actually going to have them mess up by, say, letting a villain go and it coming back to bite them, or fumbling something at a critical moment and it getting someone hurt. I'm not sure how else to describe this, so I'll just skip straight to the examples here: SCP-116 has a fantastic healing factor… but it has no joints and can't move without breaking its fragile bones, and thus cannot communicate without causing itself constant pain. SCP-166 is a succubus whose powers allow her great control over men… but she's also a nun, is greatly distressed by her very nature, and her skin is so sensitive that she gets bedsores from wearing anything. SCP-187 can see the state things will be in in the future… but she's slowly going insane because of what she sees, she has to be blindfolded in order to eat, lest she look at the food and see it as what's going to come out the other end, and the Foundation mittens her so she can't claw out her own eyes.
The third thing I want to address — and this one's important for every SCP, but just easier to screw up on with sapient stuff — is that the Foundation is not a hotel service. The Foundation is not here to coddle your SCP object while it sips cocktails on the beach and tweets about how SCP-105 is so cute. We secure. We contain. We protect. SCP objects should not be allowed any contact with the outside world, because that's a security breach. SCP objects should not be allowed out of their containment when not being transported, and should not be given access to other SCP objects, because that is a containment breach. SCP objects that lash out at staff are to be smacked down as brutally as necessary, not appeased, because to do otherwise is a failure to protect against it.
Now, for these next three points, I'd like to bring your attention specifically to the listed exceptions primarily because they demonstrate the lines that you not only should not cross, but should not attempt to meet because it's been done before. Think of these three SCP objects as defining the upper bounds of what's acceptable for each trait they represent. You should try to aim considerably below all these lines.
The first, of course, is the Able Line. Able, or SCP-076-2, is as badass as we allow, and our resident Mary Sue/Marty Stu litmus strip. If it's more badass and/or Sueish than Able, then you need to dial it back until this is no longer true.
The second is what I'll call the Bes Line. Bes, or SCP-208, is the sort of cool guy that you'd like to hang out with. He's amiable, completely benevolent, has healing powers, and helps out around the medical ward. If he wasn't based on an actual folkloric deity, he'd be downvoted into oblivion. As it is, he has pretty much completely filled our quota for the "totally approachable, straight-up benevolently magical, crazy trustworthy guy you'd like to hang out with" niche.
Third line's the Dimension-Hopping Kid Line, because SCP-507 doesn't have a name. This kid's got some damn low security. He's allowed to wander about, and the Foundation even gave him a gun that shoots rubber bullets. There's two reasons for that. First of all, the Foundation has got him so thoroughly whipped that he's basically our loyal puppy that occasionally gets spontaneously lost in other dimensions. The places he goes are the real scare here, honestly. Secondly, the nature of his uncontrolled dimension-hopping makes containment breaches not just an inevitability, but a regular inevitability through no fault of his own, so being the normal level of uptight about it is just going to give everyone involved more headaches.
All that said, good luck.