My list would include
Top spot - Turkey
2 - Pakistan
3- Iran
4- Egypt.
Its interesting to note how these countries also hold 7,8,9 and 10th position in the list of top ten armies in the world.
But still Pakistan has an edge over higly professional Iran army for it has nuclear weapons and I guess Iran's are still at a fledgling stage. And Iran's navy is atrocious or so I heard.
Interestingly Saudi army and Syrian army 're also worth a mention as they benefit from their status of quasi states of US and Russia respectively.
I still think TURKEY's army is the BEST among the muslim countries......and "secular"