From YC's current FAQ:

Q:Our group has two ideas. Can we submit two applications?

A: Ok. Just submit them from the YC accounts of different founders.

From a version of the same page from last year on archive.org:

Q: Our group has two ideas. Can we submit two applications?

A: Ok, but no more than two.

No, 3 separate applications on separate accounts.

I'm already in the launching phase of one of my ideas. While developing it I discovered 2 more ideas & found people who believe in them. We spent last weekend writing the 3 more applications and are working on mockups.

One the one hand I want to keep my focus, but on the other hand I believe each of these three are valuable.

Do you mean sending in the same application with updates? Or are you talking about sending in two separate ideas on different accounts?

I'm assuming that if they like your initial idea that they would keep tabs on the newer updated versions of your application.

If you have other ideas I'd say that it could only benefit you to send in more than one.