What if one of the parents is dead? For instance, I have two 2004 holdbacks whose mother died this past February.
Yep, we have an "inactive" flag.

(Thanks, Susan!) That could mean any number of things, but the basis of this flag is "it will not produce any more offspring." The idea is for the owner to be able to set this flag. If the snake is sold, it is not "inactive" but has only transferred ownership and can still produce offspring that are related to the offspring hatched under a previous owner.
This brings up an interesting point... If the snake is sold by person A to person B, and B decides to leave the snake's name as it is, and leave the owner as "A", then we should be able to at least allow the person (A) to change it in the database with an email request. Otherwise when they are searching for snakes owned by them, they might be finding stuff they've sold long ago. We'll have to figure out exactly how to handle this.
I want her colors reflected on my holdbacks' pedigrees, but that means I'll need to register the dead mother first, right? Can I do so, even if she is no longer alive?
Yep, snakes that are deceased can be entered so that they show up on pedigrees. If they are registered as deceased or inactive, a certificate won't be issued, of course. (This will be added to the reg forms.)
2) With some of my other holdbacks, I no longer own the sire (I sold him last fall to a local reptile store, so I don't know who owns the snake now). But I want the sire's colors on my holdbacks' pedigree -- can I still register the sold sire, even though I no longer own him?
If you don't own the snake, you can create a dummy record for him. This would allow you to put in a picture and his genotype, etc. so they'd show up on the pedigree. (It's possible that the new owner could register it under a different ID# and nobody would ever know they're the same snake, but it's better than no information at all.)
3) Several snakes in my collection have come from breeders who have already registered their snakes, but I have no idea which of their snakes were the parents of my snakes. Since I'd like for my snakes' pedigrees to go back as far as possible, how do I find out, at this point, who my snakes' parents were, whether those parents have been registered or not, and what those parents' names/registration numbers are? I'm guessing I need to contact the breeder for that info, right? However, for some of the big breeders, I can envision that it may take a huge amount of their time trying to respond to requests such as these. I hate to do that -- is there any other way?
If you have no parent info, we can't do anything on this end. If you got internal parent ID#s from the breeder, you can search the registry for them. I know that Kathy and Don are using their internal ID numbers as the Registered Names, so you would be able to find them if they're in there. For example, if you got it from Don and the mother is "10" just do a search by Registered Name for *10* and "SMR 10" would show up among the results.
If it's not in the results, we're currently making "dummy records" as placeholders for those individuals, so supply what information you do have, and we'll make and attach those dummy records to your snakes. (The pedigrees are probably not going to be a lot of use during the initial period when everyone is adding everything in random order, but next year and beyond they should get a
lot more interesting.)
4) Some of my holdbacks may be hets for genes that are not being visually expressed (for instance, some are 66% likely to be het motley). Also, I have no way of determining the parents' colors of some of the snakes I own (primarily those I've purchased from a reptile store), so some of them may be het for genes that will be revealed only after breeding. Will we be able to amend the genotypes of our registered snakes as hets become known through breeding trials?
Yes, pretty much anything on the record can be amended. Gender, genotype, notes, name, etc etc. This does require physically sending in the certificate (for proof of ownership) and if it requires a new certificate issued, it's a small fee to cover the cost of the new certificate.