Rather than asking how to use iPads in a special needs classroom I encourage you to ask the question, "What are the needs of the special ed classroom and can the iPad be a tool that can accomplish those goals."
Special ed classrooms have very specific needs and I think its important to identify those needs before you apply any tool. We use iPads in many of our special ed classrooms but only because we determined that the iPad was the best tool for certain specific goals. For other goals we use other tools.
The iPad is a fantastic tool, but it is just that... a tool. Determine the needs for your special ed classroom(s) first and then find the right tool(s).
I've worked as an ICT Tech in SEN Schools since 2006, shortly after the iPad 2 came out my previous school took them and trilled them, the success was amazing that we went on to purchase up to 35 iPads by the time I left last year, that was nearly 1 per student. I'm now in another SEN school and started to work on iPads with them and again the iPads have been great, communication has improved, the students can use them much more than a standard computer and have many apps from those who can only do simple cause and effect by one touch to complicated maths and English app's like phonics and oxford reading tree.
And I repeat what NSjoey said...
A I work with students with huge learning differences. Special needs kids are so vastly different from each other. Determine the need with a professional, then do a google search or search the app store.
Hint add this keyword "site:.edu"
example google search: site:.edu ipad apps dyslexia
B - Here is what Apple has posted:
C - AppWriter
D - I read Write ( competition to AppWriter )
E - Search for product reviews like this:
The link above lists 50 apps, but does not even mention Appwriter nor ireadwrite, nor things like phonics genius , ling apps letter tracing, nor spellingcity.com and their companion ipad app.
I've never heard of Oxford Reading Tree as suggested by others here. Dead end search on the Apple Store.