You can look at the following two articles to guide your solution
http://blog.thekid.me.uk/archive/2007/03/24/web-config-modification-manager-for-sharepoint.aspx

http://paulhorsfall.co.uk/archive/2007/03/29/How-To-Programmatically-Disable-Custom-Errors-and-Enable-Debugging-And.aspx

cheers

Thank you for the ideas. I used option two in a SharePoint application and had it deployed via the WSP. The file was successfully placed into the 12/CONFIG folder, however, the changes did not appear in the web.config file. It was then I saw the “However, this approach will not modify existing web applications” sentence. I am hoping you might know of a way to do what I am trying to acheive. I would like to deploy changes to the web.config as part of the WSP so I can have changes appropriately pushed to all of the servers on the farm. Things like application settings, database connection strings and the like could be set without having to manually update the web.config file (which could be overwritten) and could be deployed without having to manually update each of the front end servers.

I tried the stsadm.exe -o copyappbincontent command to push my changes to the web.config and it worked. Unfortunately, it pushed the changes to all of the other SharePoint sites (MySite, SSP and Central Admin) which was an undesired affect. Also, even if that was acceptable the stsadm.exe -o copyappbincontent command would have to be run on every front end server.

Any help you can provide would be appreciated.