I see we had a bit of lag this morning. Boy will I be happy when the server upgrade is complete.
If you have players that choose PCs with widely disparate alignments, and it is interfering with the game, ask yourself why.
Are they intentionally trying to stir up trouble because they like tension?
Are there player vs player issues?
Do they operate under the mistaken impression that if all the PCs are the same alignment that they need to be bestest friends and always get along?
Do they "gotta be different" because they want that attention that comes from being the troublemaker?
Why does the player(s) choose a disparate alignment? If you can find that answer, you can beging corrective measures to make your campaign better.
If the player is looking for more tension, then you need to ramp your game up so it isn't so ho-hum. This might mean making the combats tougher, but that need not be the only solution. Perhaps the player likes more uncertainty and drama. Look to Ravenloft and similar games for ways to step up your tension. Or maybe you need to add more political intrigue and mystery. Perhaps all your NPCs are too easy to get along with and you need more conflict outside the party.
If you have player vs player issues, then you need to discuss that with the players. Maybe they need to tone it down, or maybe somebody needs to leave. There have been tons of threads about problem players on EN World. If you have one, post your situation in the general discussion and you will get a lot of replies.
Now if the players operate under the notion that all the PCs always get along and everyone is just smiling-people-holding-hands, they need to think outside the box for RP. I had a game where two players were playing a Paladin and a Cleric of the same god. The PCs were the same alignment and were generally friends. But there were times when they would disagree on the proper way to handle a situation. It was some good roleplaying because both had legitimate perspectives for the PCs. They could vehemently disagree, but then they could turn around and work together. Think of all the times when you disagree with your friends about something. In the end, you are still friends right? You still trust each other despite your differences. Why can't PCs do the same? If you have a Player that has to play a PC that is different just because not everyone should get along, point out the shortsightedness of that perspective.
If you have a player that plays PCs that are different so he can get attention, you have a couple of possible issues. One is that the player is a drama queen. The other is that you are not doing as good a job at giving your PCs (and by extension your players) moments to shine. Be sure that you give each PC that moment where they are cool and the center of attention. Every PC has strengths and one of your jobs is to be sure those strengths are highlighted from time to time.
By no means is this an all-inclusive list, but I think it helps get some ideas started.
If you are beginning a campaign and you fear the disparate alignment syndrome, then I suggest that you begin with heavy conditions. There is no reason why you can't say that all PCs must come from the same region and share the same general morality/ethics. I know it sounds like it won't work, but stop and really think about it. Make it a story reason why everyone starts off like that and many players will be happy to make their character and see where the story is going to go.