If you are looking here to find out how to get Advanced Search or custom search scopes to show up then also check here.
While researching the SharePoint DelegateControl I found some misleading information on the value of the sequence attribute that should be used with a custom Feature to replace the default search box (SmallSearchInputBox). Most of the blogs say that sequence should be less than 100 to make your search control be used in place of the default. Turns out that sequence must be less than 25, not 100.
I think that many of the articles on the web may have been tested on WSS, not MOSS. MOSS has it's own Features to replace the search box.
On my server these Features also override SmallSearchInputBox:
So any custom Feature you add needs a sequence number less than 25.