A good example to illustrate some differences is a Paladin's Divine Grace, and a Blackguard's Dark Blessing.
At 2nd level, a paladin gains a bonus equal to her Charisma bonus (if any) on all saving throws.
A blackguard applies his Charisma modifier (if positive) as a bonus on all saving throws.
Note the difference. The Paladin is passing by value, but the blackguard passes by reference. The Paladin creates an entirely new unnamed bonus which happens to have the same value as his Charisma bonus, while the Blackguard takes the already-existing Charisma bonus and applies it to his saving throws.
So the Paladin's Will Save might be:
+4 (base) +2 (Wisdom) +1 (Resistance) +3 (unnamed),
while the Blackguard's is:
+4 (base) +2 (Wisdom) +1 (Resistance) +3 (Charisma).
Now, let's say we have a PrC that also applies Charisma bonus to saving throws, and both these two characters take a level in the PrC.
Now we have the Paladin/PrC:
+4 (base) +2 (Wisdom) +1 (Resistance) +3 (unnamed) +3 (Charisma),
and the Blackguard/PrC:
+4 (base) +2 (Wisdom) +1 (Resistance) +3 (Charisma) +3 (Charisma).
Note that the Blackguard/PrC now has two named bonuses that do not stack, while the Paladin has one named Charisma bonus, and one unnamed bonus equal to his Charisma bonus... which stack.
The Monk adds his Wisdom bonus to AC. So it will not stack with any other Wisdom bonus to AC; however, it will stack with a bonus equal to his Wisdom bonus to AC, should a PrC provide such.
Another one to watch out for is the Duelist, who does not add his Int bonus to AC; rather he adds his Int bonus to his Dex bonus to AC.
A Duelist with a Dex of 12 and an Int of 12 does not have an AC of:
10 (base) +1 (Dexterity) +1 (Intelligence);
rather, he has an AC of
10 (base) +2 (Dexterity),
because his Int bonus modifies his Dex bonus to AC, not his AC. So the duelist's Canny Defense will actually stack with an ability that adds Int bonus to AC, because while the bonuses have the same name, they are modifying different scores.
-Hyp.