As the GM
When starting the game, you have to set guidelines. For new groups, or players that don't know each other well, you should probably prevent all inter-character conflict whatsoever. The best way to do this is nip it in the bud. Before the campaign starts, let players know the rules:
"Just so you guys know, I want to minimize inter-character conflict for this campaign. That means that I will not accept evil characters or characters that you think will be difficult for the other players. Feel free to make loner-type or anti-social characters, but make sure they will actually care about what the party thinks of them. And definitely no backstabbing or stealing loot."
If you have already started the game and an issue crops up, then you have a more difficult task ahead of you. Players will often defend their decisions by claiming "It's what my character would do." Although this may be true, it is certainly not a justification for causing problems. You have to let your players know that this type of behavior is simply not acceptable:
"I understand that this is what your character would do, but it's causing problems for the other players, decreasing everyone's enjoyment, and making our gaming sessions a lot less fun. Let's see if we can tweak your character so he's still fun for you to play but isn't an issue in our group. I'm sure that we can find a healthy balance."
As the Instigator
I'm going to keep this short and sweet. Preventing intra-party conflict as the Instigator is as easy as asking one simple question:
"Hey, I think it would be cool and interesting if my character would do this. However, I recognize that it might cause some problems for your character. Would you be okay if my character did it? I totally understand either way."
As the Victim
First ask yourself this: Are you really the Victim? Or are you causing problems of your own? In most conflicts, both parties act as Instigators. Read the Instigator section, then come back here. I'll wait.
Okay, if you are really an angel and are the victim of another player's abuses, then you are in a tough spot. You have two options.
The first, potentially awesome, potentially blow-up-in-your-face way is to roleplay. Try and let the issue roll off your back (as the player at least), enjoy the developing character conflict, and roleplay your character. The rogue is stealing loot? Time to send him a message with a cursed item. The paladin is being a goody-two-shoes? Let him know what happens when he tries to stops you mid-rage. Wizard is actually evil? Kill him of course! While this method can be fun, it suddenly turns you into the Instigator, and thus (possibly) the problem. It can be great, or it can simply escalate the situation. Be careful.
The second, safer, and probably better option is to talk to the instigator. Let him know that the way he is playing his character might be fun for him, but it is not fun for you:
"Hey, I know you like playing your character this way but it's really causing me problems. I've been enjoying sessions less and less, and I think that without the inter-character conflict I would have a lot more fun. Do you think you could roleplay your character in a slightly different way that doesn't put our characters at odds?"
* If you have been gaming with a group of close friends for over a year, then all of these suggestions start to slide. You (hopefully) know each other well enough that you can work these things out directly, and get some great roleplaying out of it. However, if you are new to a group or not too close of friends with the guys, be sure to read this post carefully and act accordingly.