Some months ago I came across a good website that offers to search and plan your travel with mixes way of transportation... Like for example you have to plan a mixed way, like flight and bus, similar to www.fromatob.com?
rome2rio is a multimodal transport search engine that mixed flight, bus and ship.
Compared to fromatob it search much faster and cover bigger area. It also show the route of each option in the map.
(the upper one is exeter, uk-Hong kong searched by fromatob and the lower is same route searched by rome2rio)
If you want to travel within one country in Europe you can often use the train planner to get a combination of train and bus, like the Bahn site for Germany and Belgianrail for Belgium. In the UK you can use traveline for train, coach and buses, I am not sure about flights but it might work.
Non of those keeps being that helpful when crossing national borders.