Do it in a subtle manner
Probably the biggest thing to remember when designing a branded web application is that people aren't there to interact with your brand, they are there to interact with the space and platform that you've created. They want you to get out of their way and stand back while they do whatever they want to do.

Do offer utility
Users will leave if you don't offer them utility. If your application has hundreds of about or products pages, they'll leave and never come back. You application needs to make people's lives easier. People are looking for something that will make them remember their grocery shopping list or track their running progress, not to read up on the latest products.

Do define clear metrics - what is measured as success on your site?
Defining what you measure as success can be a difficult process. If you are trying to help people with their diets, is your measure of success in page views or centimetres trimmed? With an application it goes far beyond measuring trackable analytics - you need to have a clear idea of what you measure offering utility.

Do engage
It won't help you if you aren't part of the community yourself. The community managers on your site need to actively use it themselves and also engage with the community. They need to be embedded deeply into the interaction of the community and the community needs to feel them as a trusted part.

Do remember activity
When a user stumbles across your site is there something that they can DO. Can they do something on the site, you take that action and show them something new? Also, when users interact with your site, show them that. Also, show other users that  e.g. one of their friends has just lost 4 kg's. It motivates them and inspires them to interact more themselves.

You're in it for the long haul
Realise that a web application is not a campaign. It's a commitment. Web applications require time and energy. They don't end at a certain time, but they grow and evolve. Web applications that don't stick around lose their value, to a user and a brand.

Don't hard sell
Once again, subtlety plays a large role here. It is expected that a branded web application will try and sell something. When and where this happens, it needs to be subtle and without detracting from the primary utility of the site.

Don' forget about the Users
Remember that you are dealing with people. It's important that you have a constant concept of the user in the forefront of your mind. A web application is nothing without it's users. Remain focused on offering as much utility to the end user as possible. Also, listen to your users - after all, that is why the site is there - for them.

Don't build it and let it run.
This takes commitment and needs to evolve. You will probably realise that some parts of your application end up being dead zones. Luckily (through analytics) you can see where those dead zones are and try and revamp them, or ditch them entirely if they aren't working. What you start out with might be something entirely different as to what you end up with 6 months down the line. Evolvement of your product requires constant feedback from your community and a commitment to change it if it doesn't work.

Don't focus on the technology
You application must be technology agnostic. Don't use fancy frameworks of slick interfaces if it gets in the way of the functionality of the site. Remember that you are trying to sell utility - you want to offer the user something of value and not "a great experience with AJAX and an open API using REST methods".

Don't jump on the SN bandwagon
Social Networks are merely a component to a site. All social sites should have a profile and allow interaction, but that shouldn't be the sole reason for existence. Remember, people can do that on Facebook. What can't they do on Facebook? That's where you need to position your application.