I got a chance to work on the below documentation softwares recently, were pretty good. There might be some other softwares better than these, if so, let me know.

1. SQLSpec – For database documentation, it supports various databases like MS SQL Server, Oracle, Access, DB2, Sybase etc. It is very easy to use, however, customizations like excluding objects and xml commenting took me sometime. It creates MSDN help file style documents. Download link - http://www.elsasoft.org/
2. SandCastle – Free software, for .NET project documentation. Supports .NET 1.1, 2.0, 3.0 and 3.5.  It is also very easy to use and creates MSDN help file style documents.  Download it from here http://www.codeplex.com/Sandcastle and install it, and then install SandCastle Help File Builder from here http://www.codeplex.com/SHFB