I have a website in Sharepoint 2007. We use a wsp to deploy our projects. We can deploy dlls, usercontrols, features, but i don\'t know how to include new lines in the web.c
In addition, if you think about using appSettings from web.config for your site configuration values, you actually have other options as well. For various reasons web.config might not always be the best place to put your values - at least not if a "superuser", etc. is supposed to be able to change them later on. For this, you could instead use a Config Store-feature, which also scales across the farm for multiple front-end servers, etc.:
http://www.sharepointnutsandbolts.com/2008/05/introducing-sharepoint-config-store-for.html