Set Clear Priorities
Shifting priorities undercuts morale. People don't like to throw away the results of their hard work. Switching priorities can have the same effect as multitasking-nothing reaches completion. Change priorities often enough, and people will view the newest priority as "flavor of the day." The reality of business is that external events may dictate changes. Iterative development, with its three-to-six-week sprints, is one of the ways to manage for accomplishment in a shifting environment. If your organization can't hold to one set of priorities for three weeks, it's going to be hard to make forward progress in any direction.
This is one of the most powerful morale building tools in a manager's toolkit. Find out what's getting in the way and work to remove the impediment. When people see their managers are making it easier for them to work, morale goes up. Managers can't always remove every obstacle. Let people know what you're trying, and be honest if you can't fix it.
Don't Over Specify
Give people the goal, set them in the right direction, and let them decide how to get there. People will come up with a surprising number of creative ways to achieve the goal. Telling people both what to do and how to do it stifles morale, and defeats productivity. There's only one thing more de-motivating than over specifying the goal and the method: over specifying the method, and not articulating the goal.
Deal with the Un-jellers
It's hard enough to build software without someone actively working against the goal. It's a manager's job to field the best team possible. If there is a person whose interpersonal skills are making life hell for the rest of the team, deal with it. Sometimes that means moving someone off the team. Never underestimate the impact that an un-jeller will have on the team.
Negotiate Reasonable Deadlines
We all know that we don't always get to choose the release date. If you're stuck with a hard date, prioritize the requirements and negotiate scope. Knowing from the get-go that the schedule is impossible to meet is not very motivating.
If you're stuck with a hard date and a hard scope, talk to your team. Tell them you want everyone to work as hard as possible and that you have serious concerns about meeting the goals even if everyone does their best. Ask the team if they have any ideas on how to make the project work. Knowing that you recognize the situation the project is in will help the team remain focused and energized. Working reasonable hours is a better strategy for reaching goals than going on the fabled death march.
Pep talks, contests, and certificates won't build morale. They can be fun when things are going well, but when your team is in the pits, they contribute to cynicism, which widens a chasm between practitioners and management. There's no short-term fix or magic formula for boosting morale, but old-fashioned, effective management may just do the trick.