I soaked a three of cups of dried navy beans overnight to use in a baked bean recipe, and now I see that the recipe only needs two cups of dried beans.  Can I freeze the ones I don't need for some future use?

Dried beans that have been soaked can be drained and frozen as is, or they can be boiled first and then frozen.  You may find after freezing that some of the beans have broken open.  Depending on what you end up using them for, this may not be be desirable.  They will probably be alright for a future batch of baked beans, though.

If you chose to boil them before freezing, you need to decide whether you want to then drain them, or freeze them in the boiling liquid.  Either way will work, and largely depends on whether you want to use the boiling liquid in the final recipe.  You also should under cook them a bit, so that they are a little firmer than el dente.

If you use the quick soak method, where you boil the beans for a few minutes and then allow then to stand off heat for an hour, you can still freeze the beans at that point.  Just remember to allow them to cool down to room temperature before putting them into the freezer.

You can also freeze lima beans, chickpeas and other dried beans or peas that require pre-soaking before use.

In any case, you should probably use the beans or peas within a month or two after freezing.