Some of the most important things of the ETL that you must document:

* data mapping (given a certain output column, which are the contributing input columns)

* information liquidity model: describes the "flow" of the data through the whole ETL process

Powerdesigner (a data modelling tool) has the capabilities to document this in great detail (even create the deployment scripts for the databases), but it is a rather complex tool.

And of course, your code should document itself. Add annotations in your package, add in line comments in your T-SQL and .NET code.