Every year Microsoft sends out a survey which the execs and managers use to help get the pulse of the worker bees. One of the areas where our group didn't do as well as we would have liked was around inclusion / team cohesion. My manager asked me what I thought we could do in this area, and here are my generalized thoughts.
Common Goal and Purpose
To start with, there must be an underlying goal which is understood and believed. If the goal is not clear and concise, then there is no coordinated direction. This leads to wasted work (if it isn't truly important to the vision) and marginalizes peoples' contributions or places greater rewards on other team members. Dissatisfaction and discord can also set in if the team doesn't think the goal is reachable or doesn't agree with its direction. The vision is the foundation which your team needs to rally behind and gets everyone marching in the same direction. Changes are needed if people don't believe or understand why their work is important. Often this can be helped by improving communication or cutting unnecessary features and focusing the team on what is important.
Good communication is fundamental in ensuring everybody feels included, this means that decisions which impact team members must be understood and believed. Ensure that decisions are not created a vacuum, at the wrong level, or by the wrong people. This is where strong leaders and program managers pay off, they will help drive the features and make sure all the necessary players are informed and brought in on decisions. Additionally, small changes such as office layouts and organization chart optimizations can help foster easier coordination between the individuals who are working on related technologies.
Rewards and Motivation
Exclusion is a sure way to alienate someone from the team. Recognition, cool projects, gifts, benefits, etc. all need to be appropriately spread around. Militaries across the world have all used unit citations to help build a collective level of pride in a team. It doesn't matter how much an individual contributed (if at all) because, when recognized, everyone in the unit got them. Individual rewards have their time and place but they can weaken the overall team cohesion. Also, make sure that events, entertainment, food options, etc. are all open and inclusive. You definitely don't want a morale event to do more harm than good by alienating the very individuals you most desperately need to improve the morale on.
All of these things can make an impact to how tightly an individual will be integrated within an organization; all it takes is a good leader to help kick some of these into place. But keep in mind that one of the underlying concepts here is empowerment. Do you encourage the employee to make a meaningful difference, or are they just tools to get a job done?