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For the love of Science!
I have read about 5 different methods of germinating Nep seeds, and have decided that I am going to give it a GO. Going to order a couple species of Lowland neps, and give it a shot. The site I am looking at currently offers Rafflesiana, Tenax, Albomarginata, Madagascariensis, Truncata, and a few others. Is one of these any easier than others to grow from seed?

Most guides advise just tossing all the seeds into a single pot, and transplanting them once they start to crowd, or reach a certain point.

My question is: Why wouldn't you just plant them individually in smaller pots, and spare the seedlings the stress of handling and re-potting when they are very young and fragile? I would think it would be better to have separate pots, in case of fungus, or other problems that might spread if they were grown in the same pot together.

Am I missing something?
You can do that, but it's often a good idea to repot your seedlings every six months or so, or whenever the media is beginning to noticeably decay. It may stress the seedlings out slightly, but they will grow much better when not competing with anaerobes. With this in mind, planting individual seeds in individual cells becomes a spatial constraint and very time consuming, particularly when you expect to repot them soon anyway.
1) If you plant each seed in its own pot and the germination rate is under 10% (it can happen with purchased seed, as its viability decreases rapidly after harvest) then for every one pot with a seedling, you will have nine empty ones.
2) I have yet to harm even the tiniest seedling when transplanting it from its starter pot - there is really little to be concerned about. You're overthinking the process ;-) Save your energy for the things that matter more.

Plus what Mat said.
I put quite a few seeds per pot, I just make sure they don't touch as seeds
I am also looking for good sources of Lowland Nepenthes seed (any kind will do), where I can be assured it is fresh seed. Preferably from the US or Canada, so I know it isn't poached.
You do know that seed imported into the US requires a phytosanitary certificate and/or a import permit. The permits are free (except for CITES species) and if you are importing seeds within quantity and weight limits (Small Seed Lots) a phytosanitary certificate is not required. There are numerous threads on the subject.
Ideally, I'm hoping to find domestic growers with seeds available.
Ideally, I'm hoping to find domestic growers with seeds available.

Well, some people on here will occasionally do give aways of extra seeds. That is how I got some.
Yeah, once I get the hang of it, and have some success germinating, getting my hands on specific seeds and hybrids will be fun and games, too.