Hello,
I'm the developer of PokerCruncher. I'll comment on just the PokerCruncher part of this post and will leave the rest for others to give input on.
The iPhone, iPad, and Android versions of PokerCruncher have 1 hand ordering, the same as PokerStove's hand ordering, where hands are ranked according to preflop all-in equity vs. 3 random hands. This has become a de-facto standard hand ordering and is a good general purpose ordering for many types of game situations.
The Mac-Expert version of PokerCruncher has 8 different hand orderings, listed on this page:
http://www.pokercruncher.com/ipPoker...lHandOrderings
You'll want to use different orderings for different types of game situations. For example when deciding if you want to move all-in preflop in a heads-up situation, the Sklansky-Karlson(Chubukov) All-In No-Limit Hold'em Rankings would be the best ordering to use. This ordering gives a higher ranking to Ax hands, and a lower ranking to suited connector hands, than the PokerStove ordering. For example 54s has higher value in a general game situation where you're seeing a flop against at least several opponents than in a preflop all-in heads-up situation. The above webpage has descriptions of the 8 orderings.