I keep the source to generate the stored procedures, tables, views, functions, etc... in the version control system. The scripts are much cleaner and easier to control than the auto-generated variety. Too many SQL Server DBA's tend to use the Server itself as the code repository (a bad idea from a maintenance perspective).

Just one note if you are going to generate the scripts => remember to drop the objects in the reverse order that you created them - otherwise you run into object dependency problems (e.g. can't delete a table that is currently acting as a FK). I've noticed in the past that the auto-generated scripts from SQLServer did not always maintain the correct order of drop and create - meaning you had a fairly arduous task trying to get things manually in the right order. Perhaps they've fixed that on the later versions (it's been awhile since I've used the feature).