Try to opt for Webkit as it is used by many different browsers (Konqueror, Safari and Google chrome). This makes Webkit more versatile and more adaptable to other needs.
The development of Gecko is very tied with Firefox. A lot of modifications made to Gecko are done because Firefox dictates them. For instance, Firefox 3 decided that it was going to block all self signed certificates for security purposes. The implementation has been done into Gecko's engine which means that any application that decides to embed Gecko has this security constraint added to them.
If you can stay with Webkit as it mainly a rendering engine for HTML pages. That's been developed with the intention to be used among different web browser. While Gecko is primarily the rendering engine of a single browser which just happens to offer an API for embedding.
