InShidduchimFollower: Just a few pointers that I don't think were mentioned in the "looking-into-guy-thread".
1. Try to ask open-ended questions (avoid questions that can be answered with yes or no). For ex: Instead of asking "Is he a talkative guy?" you would say "Can you tell me a little about his personality?" The person will usually share the things about his personality that immediately come to mind.
2. Ask the person you're talking to (in the beginning of the conversation) how well he knows that person. This is a good idea for two reasons: First, you get an idea for what kind of questions you can ask this reference, based on how well he knows the guy you're looking into. Second, if you were told that they're close, and the reference claims he knows him "vaguely, a little bit, not really well, etc." it may be a red flag where he's trying to get out of having to provide detailed info.
3. When it comes to deal breakers, the following could be very helpful: Tell the person "I cannot see myself happy with a guy who does/has/is XYZ. Do you know if that's the case with him?" or "In order for me to respect my husband he would need to do/be/have XYZ." If the reference truly cares about his friend, they will somehow get the message accross that this shidduch might not be the best idea. (FYI-I've b"H gotten people to tell me pretty sensitive things about their friends this way. Nobody want their friend to be unhappy. Sometimes they will not tell you outright, but will contact their friend and let him know that this girl who's checking into him is not for him. I've seen it work both ways.)
4. Take notes when you speak to references. Make sure that the info you're getting from different people don't contradict each other. Something isn't right if two people claim he's more to the quiet side and the other two seem to think he's the life of the party.
5. This point is so, so important: Don't forget that everything you're told is nothing more than someone's opinion. It's important to understand where they're coming from. When I'm told things like "He's ____ type, but more liberal", " He's very mature", "He's a real family guy", "He's very thoughtful"...alwaysrespond with a question like "Can you give me an example where you see that?" or "Can you explain what liberal means to you in this context?". What someone else considers unbelievably thoughtful may be basic mentchlichkeit to you. And since you don't know who you're talking to, it's important to get them to elaborate as much as possible.
6. When I know that I'm talking to someone who is really close to person I'm looking into, ask them directly "What kind of girl is he looking for?" There is no better question in the world that'll help you get an idea whether or not this thing could work. But it's only fair to ask if that person really knows the guy well.
7. Before you make the phone call, have a list of questions on hand. The link to thinkingBYgirl's post is an excellent place to start. As you read through her list, you will think of your own questions.
8. You asked how to tell what really lies behind their words. When they start using cliches and one word answers, gently push for elaboration.
9. Before you pick up that phone, talk to Hashem and ask for His help. May you be given the Siyatta Dishmaya to know what to ask, know how to listen, and ultimately find your bashert soon. Good luck!!