What Smartboard challenges are unique to the Judaic classroom?
Two immediately come to mind: the use of Hebrew on the Smartboard, and the lack of resources for Judaic lessons.

Lack of Resources
It's only in the past few years that Limudei Kodesh has embarked on the Smartboard revolution, and resources such as notebook files and Smartboard-based lesson plans are naturally more difficult to find than their limudei chol counterparts. This situation should change rapidly, however, as Smartboards become more ubiquitous in Jewish schools and teachers create more lessons.

Part of the purpose of this wikibook is to bring these resources together for teachers, to make them easy to find and access. The more this project grows, the more likely it will be that teachers will no longer have to lament the fact that there are so few resources out there. It's a temporary problem that will be resolved, sooner or later.

For a list of current resources, click here.

Hebrew on the Smartboard
A number of posters on the AVI CHAI Ed Tech blog have posted their experiences in working with Hebrew.
Instead of reiterating them here, take a look for yourself:

http://edtechexp.blogspot.com/2008/03/hebrew-texts-on-notebook-smartboard-and.html
http://edtechexp.blogspot.com/2008/02/getting-hebrew-text-right.html

Whether or not to use Notebook despite the difficulty in Hebrew usage depends a great deal on how much Hebrew text you're dealing with, how important it is to manipulate it in Notebook, and whether you find a solution (such as those described in the above posts) that works for you. I personally find that writing in Davka, then pasting into Word, then copying again and pasting into Notebook, works well for me. I can do this with any size block of text. I will typically make any necessary changes in Davka before getting it into Notebook, so I'm not actually doing any editing in Notebook.

I have heard that the Mac version of Notebook handles Hebrew better, though I have not been able to verify this myself.

The Lesson Activity Toolkit at this time does not support Hebrew for many of its flash-based tools--the ones that have just limited fonts available. I have tried dragging Hebrew words into tools that support images, hoping it would be treated as a picture. It seemed to work, but when I saved, exited and then opened up the document again, my Hebrew words all disappeared. So, be cautious.

About Hebrew on Promthean see here.