I have developed a generic app, which can ne customized for clients. Each app should be available in the app store.
Any idea what is the best way to deploy the different apps? This is of course also necessary on app updates.
Only the package name, some graphics and some settings change for different Apps. The Code will be the same for all.
Consider deploying your app as a framework, static library or CocoaPod. The clients should be able to use your framework/pod to customize the appearance (and anything else) and publish their apps.
CocoaPods: If your project is in progress and your client is using it, I wouldn't recommend it. Pods are great way for managing dependencies mostly if dependencies are not going to change on nightly basis. Also you'll have to make a few decisions about how to integrate it with your source control. If you and your clients will be working on their client app and pods simultanously. They'll most likely have to get your pods in a workspace, which defeats the purpose of pods. (If somebody knows a better way around editing pods and project simultanously, please let me know as well.)
Static Library/Frameworks: Rey Wenderlich has a good tutorial for creating frameworks. http://www.raywenderlich.com/65964/create-a-framework-for-ios