The following example shows how to set up Dependency Injection using Ninject as an IoC container.
First add a CustomModule class to your WebJob project, and add any dependency bindings there.
public class CustomModule : NinjectModule
{
    public override void Load()
    {
        Bind<IMyInterface>().To<MyService>();
    }
}
Then create a JobActivator class:
class JobActivator : IJobActivator
{
    private readonly IKernel _container;
    public JobActivator(IKernel container)
    {
        _container = container;
    }
    public T CreateInstance<T>()
    {
        return _container.Get<T>();
    }
}
When you set up the JobHost in the Program class' Main function, add the JobActivator to the JobHostConfiguration
public class Program
{
    private static void Main(string[] args)
    {
        //Set up DI
        var module = new CustomModule();
        var kernel = new StandardKernel(module);
        //Configure JobHost
        var storageConnectionString = "connection_string_goes_here";
        var config = new JobHostConfiguration(storageConnectionString) { JobActivator = new JobActivator(kernel) };
        //Pass configuration to JobJost
        var host = new JobHost(config);
        // The following code ensures that the WebJob will be running continuously
        host.RunAndBlock();
    }
}
Finally in the Functions.cs class, inject your services.
public class Functions
{
    private readonly IMyInterface _myService;
    public Functions(IMyInterface myService)
    {
        _myService = myService;
    }
    public void ProcessItem([QueueTrigger("queue_name")] string item)
    {
        _myService .Process(item);
    }
}