Don JOhnston has been making educational software for special populations *forever* (okay, since you could only get ed. software for your Apple computers) and they've got an excellent line of products. They also carry thigns they don't make that work for LD kids.
Read, Write and Type software is an excellent piece of software for learning keyboarding and developing/reinforcing phonics skills; the keyboarding and reading are tied together. www.readwritetype.com
Sunburst has some good software -- if the Read Write & Type is too young for your kid, Type to Learn and Type for FUn are good.
Some of their math programs are very good; others are okay. If you find good math software, please post & let me know. I'm still looking.
As he gets older, look at TextHelp! to use with the computer to help with writing.
Lexialearning is another specialized company that makes the best reading software I've every used; www.rlac.com carries that and many other great materials for LD kids.
My other main source for materials, though not generally software, is Educators Publishing Services (http://www.epsbooks.com).