Is there any software that deals with learning ancient Greek?
No, I don’t know of any, sorry. I looked around for awhile and gave up, deciding to do it the hard way, the same as my ancestors. You know sonny, back in my day we didn’t have these fancy-schmancy computers … 
I thought about making my own set of flashcards for a commercial program such as Before You Know It (www.BYKI.com). I don’t know if that particular program would allow me to make tables for declensions and conjugations.
Though I have found a reference to this on a mailing list, I have not yet tried it:
http://www.kalos-software.com/
Perhaps it suits your needs.
What are you looking for? If it is just a flash card program there are a number created for Koine Greek learning. Most programs allow you to setup your own word lists.
A few flash card packages
www.teknia.com - free software
www.pdascholar.com - Palm / PocketPC software
http://s91279732.onlinehome.us/flash/ - Flash Pro
This is a very very strange program. I have played around with it alittle bit. Hard to say how effective it is, it also might give you nightmares!
It’s free though. 
If you count a website as ‘software’, you should definitely check out
socrates.berkeley.edu/~ancgreek
This is the website that accompanies Mastronarde’s textbook, but morphology and vocabulary will be what anybody needs.
You can order a CD if you want to use these materials off line.
More websites: www.greekgrammar.com
Kalos is no good. My professor recommended it to me and after using it a while she discovered some grave errors in how they came to some of their forms for the verbs.
Kalos is excellent. I use it daily.