Since I was discussing this recently, I figured I'd compile my thoughts about it.
One of the main paradoxes of any sort of fan-design is how people will sit down and design a character to look as unique as they can, yet the result is very rarely memorable. I think a big part of the reason for this is that they forget about the Silhouette.
The reason for this, I think, is that people plan their characters out like images, not like characters. They try to fill all the negative space, so the characters end up looking really cool (well, "cool") in a generic solo shot, but as soon as they have to actually interact with other characters or with the world, they end up looking like a big colourful rectangle more than anything else. A bunch of fan-characters together ends up looking like a bunch of guys cosplaying as a quilt.
Leaving aside the "Sparkledog" school of design, (something you often see among furries, where they'll dump a bunch of neon colours on their fursona to make him stand out, with the result that the character looks like any number of generic technicolour furries....), this is another area where I think the problem is that people think of the characters as images, rather than elements to be included in an images.
So, even if they don't go overboard with it, they end up putting a bit more colour than the character actually need. The result being, again, a character that looks good on its own, but stick out like a sore thumb next to the canon characters.
When it comes to ponies, I'd say that the rule of thumb is one colour for the coat, max three, prefferably one, for the mane, unless there's a really good reason to break the formula. (Rainbow Dash for example, since the colours of the rainbow is usually seen as one "unit". In practice, RDs mane has only one colour, and that colour is "all of them")
I'm becoming a little more tolerant of coat markings, I was actually regretting for the longest time to give my character his "snout stain", but I've softened on this a big. Spots and markings aren't unheard of, just not common. I'd say they are okay, but only if they got a character-related reason to be there (and "it looks cool" is not a character-related reason.)
With Owly, the intention was to make him look a bit bird-like, hence why he's "owly. Most of the time, it doesn't really work, and it looks more like he has a scruffy blonde five-o-clock shadow... which is what I often have IRL being blonde and generally lazy, so it still works.
I can't really help you with things like what colour clashes with what. I've never got the hang of it, and my opinion on some seems to differ from the norm. And anyway, the thing about designing characters is that their colours CAN clash, if there's a reason for it. Clashing colours will make the character look a bit mismatched and deranged, so it should be used with caution.
The only thing you really need to know, however, is complimentary colour. It's the colour with the same saturation, but the completely opposite hue. Basically, it's what the colour would look like on a negative (people still know what photographic film is, right?)
Complementary colours make each other stand out really well, something that' useful to keep in mind for design. However, pure complimentary colours stand out TOO well, on a character, the effect becomes eerie.
Taking advantage of this is a good way to recreate the feeling of reading about a Mary Sue characters "vivid azure eyes" in a visual medium. In other words, you should prolly avoid it unless it is abislutely necessery for character-related reasons.
Actually, the side effect of this fact is kinda amusing to me. Y'see, purple eyes are a rather popular MAry Sue characteristic, but with ponies it's actually a fairly common colour. I think partially because very few ponies are green, but many are some variation of red or blue, meaning that purple will blend pretty well with mot coat-colours without sticking out too much.
Colours are often divided into "hot" and "cool" colours, with hot colours including red and yellow and cool colours including blue and green. For a balanced character, I'd say that using either the combination hot-hot-cool (two hot colours, one cool) or cool-cool-hot in their colour scheme is a good idea, with the odd colour out usually being the eyecolour.
The reason it's called hot and cool colours is cus that's the association we have in our minds to them. Red, orange and yellow reminds us of fire, heat, danger, anger, that sort of thing and blue, green and cyan reminds us of water, cold, calm, sadness and things like that.
Mixing in a cool colour with the hot ones help "ground" the character, at least in my mind. It'll make them seem more "natural" whereas having only hot or cool colours makes the characters look a bit eerie, like they are fire or ice elementals. This, I think is another reason why purple is a commonly used colour, it sorta straddles the line between hot and cool and can be used to subtly shift the balance back a little.
Notice that Twilight are among the only ponies with about the same eyecolour as coat colour? It works for her cus purple doesnt necesserily have any associations to either hot nor cool, but it wouldnt work too much for anyone else, unless their entire personality revolves around a colour-indicated trait.
3. Character-related reasons
This is a weasel-word Ive used troughout this, mostly cus if I say "you gotta have a good reason to do it" some might think "I got a good reason, it looks cool!" It might look "cool", but it has no point unless it tells you something about the character.
The problem with a lot of "cool" designs is that what little it tells about the character, it's either horribly stereotypical or it says something that the creator didn't intend to say.
A typical Mary Sue character design, for example, would tell me that this is a character who tries too hard to be noticed, who desperately want to be special, but in the end is just like everyone else. Needless to say, this usually isn't what the creators intend to say with the design, at least not consciously.
Same with dark colours. In the ponyverse, true black is usually reserved for genuinely Evil characters. Capital T Evil, rotten to the core, either trough corruption or else by it being their nature. But in the OCverse, its usually used to tell me that this character is a brooding antihero, which might just be one of the most boring character stereotypes ever.
So, what I mean with "character-related reasons" is simply that if the character is interesting, and the choice you make helps to visually represent the character, then go for it. Jmjs "Darth Pinkamena" character for example, breaks the rule of not using too dark colours, but the point of the character is that she resembled Pinkie, only turned evil, which is an amusing juxtaposition if nothing else. So in this case, dark colours help drive that point home.
Making an exception for character-related reasons is the best "second-tier advice" I can give. (Second-tier advice is what ive come to call writing tips that are useful for people who already know the chlichés, but struggle to evolve past simply avoiding them into knowing where and when to use them.)
A common mistake I see people who knows about all the shit I've said before is that they'll make BLAND characters, characters that look like generic background ponies. The point of an OC should be to add something interesting to the universe, at least in the cases where the OC is important to the plot and not just background. The audience should be able to look at the character and go "okay, this is a character I'm interested in reading more about."
Wrapping it all up, to make a good OC, at least by my estimation, pay attention to the silhouette, use colours with care and if you really wanna make him stand out from the pack in a GOOD way, give him something character-specific rather that something generically cool.
A final note about cutie marks. Some designs are much easier to WRITE about than to draw. It's easy to for example that a characters cutie mark is a witch on a broomstick silhouetted against the moon, but if you are to draw this, youll have to draw a whole entire image worth of stuff just for that little detail. And in the end it's going to look way too detailed to be a cutie mark out of the show.
Other designs might be easier to do, but harder to do well, like "half a comedy mask cutie mark, half a tragedy one". In practice, all you're going to end up with is a rather weird-looking assymetrical mask that doesnt even look like a face, cus faces can't smile and frown at the same time.
This isn't necesserily a problem when it comes to stories, cus in text you can do things like that and it works. It becomes a problem, however, when a guy named Louis decides to do an illustrated audio adaption of your story and asks a swedish amateur cartoonist to illustrate a chapter, to take an example completely and utterly at random...