Which authentication and authorization schemes are you using - and why?
Actually, the answer is probably a combination of 1 and 3.
You can take advantage of a lot of the tools and features that the framework provides for you by writing a membership, role or profile provider if the default options don't quite go as far as you'd like.
We've done just that on a number of client sites - for example one of our clients has most of their users stored as Commerce Server users, and use the Commerce Server profile system, so we wrote a membership and profile provider to talk to those datastores - a fairly simple excercise.
Most people are probably going for 3 because of the need to authenticate over raw TCP - this introduces a layer beyond that of the standard ASP.NET membership providers.
Most of what MS produce is "ok" or "good enough", but there will always be edge cases where you want to do something "not quite standard" that mean you end up rolling your own. I guess to have something beyond "Basic Auth" or "Windows Auth" that was simple for your average developer to understand, they took the sensible option of "lets just build this for the web".
If you take a look at the numerous ways you can authenticate against a WCF service, you'll see what I mean - these are designed to handle different transport mechanisms, and are therefore much more complex.
That said, the default roles and profile providers are fairly limited (roles: no hierarchy, so you need to check for each possible role, or explicitly assign each role to the user; profiles: all stored in one field as comma seperated values - not easy to find all users who've got a value set).
We use (3). Actually that helped us in an integration scenery to have accounts in sync with
- business processes
- Other systems (not all on the same technology stack (ASP.NET))
On a recent project we extended the ASP.NET membership provider (wrote a custom provider) with the intent of using some of the role based controls for managing permissions. Now that the project has matured sufficiently, we're finding that the controls are not flexible enough for our requirements, and to some extent we're regretting going down the MS membership path. Rolling your own authentication if you have the time to architect it correctly is going to be the best option.
It sounds like your app is a bit of a hybrid in that you're serving internal and external customers, but perhaps also give some consideration to integrating OpenID for your external customers. There are some great ASP.NET OpenID controls that really makes handling new accounts for external customers a no brainer. This of course depends on how 'public' your application is.