[lusr]

Another fun complication: database stored procedures implemented with non-SQL code. I worked on a project where the client's dedicated SQL ninjas managed to bring the time to process daily extracts from the data warehouse down to 2min from 45min by switching over to CLR (.NET) implementations of the calculations being performed on SQL Server 2005.

IIRC the issue was simply that MSSQL 2005 is just plain slow at doing calculations compared to C# code (the calculations were complex financial models involving large amounts of data and inter-dependencies between that data in calculations, so shipping the raw data to an application was not a viable option).