What does it mean when he stares you dead in the eye?

Strangely enough, this question can be a god question based on where you come from and what your culture believes. In many African cultures, to stare an elder in the eye means to challenge him and his authority. It is NOT a good thing, and is one of the ultimate signs of disrespect. You're basically lowering him/her to your own level.
For most other cultures, though, it means that he respects you, and that he is actually listening to you rather than just letting the words drift through one ear and out the other. It is a good thing, so don't worry. Does it mean that he likes you(if that's what you meant by this question)? Not really, just that he respects you enough to pay attention.

When speaking to an individual you want them to look you right in the eyes, if he avoids eye contact then we have a issue or he is really shy

When I stare into a girls eyes I am trying to understand what she is saying and create a connection between me and this girl but that's me I don't know about anyone else

He's trying not to look at your BOOBS! O. K maybe that, but he is also probably trying to show he's interested in what your saying. I fhe's looking at you scarily in the eyes and he knows you feel a bit uneasy or weird, he may be playng it up, trying to make you laugh (meaning he likes you)

As well as meaning that they are being honest it could mean another 2 things.
The 1st one would be that he is trying to intimidate you, but that's highly unlikely as you said he was your friend.
Another one is that he could like you. Holding eye contact is a way of showing that you like someone in some cases.
But it could be any of those things.

It means that he's honest with you. When people stare you in the eyes during a conversation it means that they're listening to you intently and that they're being honest with you.