How many of each seed should I save? I'm using the VST and lately have been trying to save 15 of each seed, but I'm scared to death that I'm going to lose all the seeds in the VST, like it's done before.

I've been saving extra of the Citrus Ball Cactus, because I've read that it's used in a lot of the crosses.

I have all three seed boxes in the game, and have been thinking about saving one of each seed in it, so if anything happens to the VST, I'll have something to self pollinate and start over again.

As you mentioned, it only takes 1 seed of each species you want to save, since you can always grow it and create more seeds by self-pollination. If you want to be very safe, store a few extras in case you forget to check on your game and accidentally cause a few plants to die. It doesn't hurt anything to save more than that, but the VST file will be larger as you start saving more and more seeds.

You can also back up the VST file, in much the same fashion as the savegame files, so that if anything bad does happen, you can restore the VST file from the backup. You can find out more about backing those files up in Borg's instructions for VST.

Why weren't there enough seed trays for all the seeds in the first place? I'm playing this game again, but now all three seed trays are full and I have lost interest because of it. Seems like it would have been easy to just incorporate more seed trays in the game. I don't want to download the mod, but I don't want to throw out any seeds.