I think you could skill and abilities checks to alloe your characters access to more areas or further information.
For example, lets say your chap/party enters a wilderness or an unknown ruin area. Depending on Spot / Listen / Search you woul be able to identify some hidden entrance or hidden objects that can unlock areas that offer either some loot items, safe rest or meeting with an hermit.
Or lets say you are on a mission to rescue some one hostage to a maddened wizard. The final encounter is not hostile at first. Based on some book you managed to read (again, due to higher lore or spellcraft), you learn that if you go invisible and talk to the Wiz, he will believe he is hearing voices. Talking to him allows you to choose some options more fitting to your alignment: a) tell him to take a potion an cure him [+5 pts to Good];
tell him to free hostage; or c) command to commit suicide out of his madness [+5 pts to Evil]. Killing him allows you to get a key to some of his stash, but curing him grants you gratitude and a map to some adventuring chutiya-giri...
Or some conversation with a mini-plot chap could give you an extra option based on either Cha, Int or Wis... I miss this kind of stuff A LOT!