Can you give more details about the webservices which are running and the general setup?

I am not completely sure what you mean with business logic, but generally I'd say that no sensitive data or generally data, which is not meant for public, should be stored on a webserver, even if it is not directly accessable or visible.

If you have some time to spend I would recommend you the book The Web Application Hacker's Handbook: Discovering and Exploiting Security Flaws.
Beside the mentioned book this whitepaper from NIST (National Institute of Standards and Technology) might interest you too.

For a web app i usually start with dirbuster and grendel scan, then follow up with manual testing...

w3af - the Web Application Attack and Audit Framework, it takes a bit of fiddling to set-up refer to the user manual for the install instructions, once you have it up and running you can just target the site and tell it to grep and mangle etc. Any holes it'll find them and cough them up in a report, I tried it out and found it finds disclosed as well as undisclosed vulnerabilities on one site I was asked to test I found that even though they where using VERISIGN certificates the site still coughed out credit card details. That made them go back to the drawing board.

It also comes with a Fuzzer which seems to be handy...

http://w3af.sourceforge.net/

w3af provides plugin writers with these features:

urllib2 wrapper
    In order to send requests to te remote server w3af uses urllib2. The xUrllib module of w3af is a wrapper of urllib2 to make the plugin writer life easier, using this wrapper a plugin writer can forget about proxy's, proxy auth, basic/digest auth, etc. This is the complete list of features provided by xUrllib:

         - Proxy
         - Proxy auth ( basic and digest )
         - Site auth ( basic and digest )
         - Gracefully handle timeouts
         - UserAgent faking
         - Add custom headers to requests
         - Cookie handling
         - Local cache for GET and HEAD requests
         - Local dns cache, this will speed up scannings. Only one request is made to the DNS server
         - Keep-alive support fot http and https connections
         - File upload using multipart POST requests
         - SSL certificate support

Output Management
    w3af provides plugin writers with an abstraction layer for data output using the Output Manager. The output manager can also be extended using plugins and can be used for writing results to a txt/html file or sending them over the network using scp, the options are endless. Available ouput plugins are:
         - Console
         - Text file

Web Service support
    w3af knows how to parse WSDL files, and audit webservices. Plugin developers can write a simple plugin that will be able to find bugs in web services and also in common HTTP applications.

HTTP headers fuzzing
    w3af supports finding bugs in HTTP headers with great ease!

IPC
    IPC ( inter plugin communication ) can easily be done using the knowledge base, another w3af feature thats really usefull for plugin developers.

Session saving
    Framework parameters can be saved to a file using the sessionManager. After that, you can load the settings and start the same scan again without configuring all parameters.

Fuzzer
    Right now w3af has a really simple fuzzer, but we have plans to extend it. Fuzzers are great, we know it.

HTML / WML parsing
    w3af provides HTML / WML parsing features that are really easy to use.

Thanks for the replies.

Yep that's the direction I was thinking of. What are the .net alternatives?