Simple answer... a web application is an application accessed via a web browser (ie, firefox, chrome, safari, opera...).
A web application can be as simple as HTML for displa…ying formatted text, and a complex as cgi, php, or .net which allow for database, webservice access..
Embedded application on the other hand can mean a lot of different things to a lot of different people, but since the first part of your question was in regards to web applications, I'll assume that the second part of your question is also in the realm of web..
An embedded web application is essentialy a plug in of sorts that allow you to use other apps in your web application simply by using one or 2 lines of code that link to other areas where the full source code is stored. Myspace is an amazing example of this. Any page that you see a video, or a game is an example of an embedded application. ( Full Answer )