Tosha touched on some of the tendencies people have noticed with various morphs. There has been speculation about certain morphs not producing a "super" form because it is fatal or causes egg death. However, this is only speculation... just because something has not been done is not proof that it can't be.
And out crossing is a very important factor in any vertebrate related breeding program. With pythons you can breed the offspring back to their sire or dam and sometimes even the second generation back to their "grandparents". Beyond that level of inbreeding I personally wouldn't recommend and at that point there would be little need to do so because by then you should have produced a number of genetically diverse individuals to select from.
As far as specific "quirks" that various breeders and keepers have noticed, here is a quick (but most likely not comprehensive) list:
Spiders: Sometimes display a tremor or head wobble. Many, if not most, individuals out grow this. Also, many people have noticed the tendency for spiders to be more "out going" personality-wise and also to be fairly hardy feeders.
Caramel: Tail and (sometimes) back kinks. Depending on the severity this may not be anything more than a cosmetic problem. If the kink is in the tail past the cloaka generally there is no problem with the snake being able to breed or pass stools. Anything above the cloaka should definitely be checked by a vet.
Piebald: Some have remarked that their Piebalds or Het. Piebalds take longer to raise to breeding size (versus other ball pythons in their collection) due to their finicky feeding response. This may just be coincidence since other people have remarked how their Pieds are great feeders.
Homozygous (Super) Black or Cinnamon Pastels: Have a tendency to produce young with more of a "duck bill" look. These individuals behave, feed, and reproduce just fine, but their face has a more squat look to it. Their "snouts" are shorter and broader. Some individuals also have a bug-eyed look to them.
All in all, beyond the kinked spines most of the "quirks" that are found in the various morphs have not proved to adversely affect the animals health. Be selective about the individual pythons you purchase, ask a million and one questions, and never complete a deal you feel even the slightest bit hesitant about. When it is all said and done and you are ready to breed be sure you have an out crossing plan factored into your breeding program and you should be fine.