Ryan Air is a point to poiunt airline. So you will have to check in each time you fly. So when booking your flight you will have to pay the fee's.

With Ryan Air you have to realise that you are on a bus with wings. If you are familliar with the service and it is a penny flight then its worth it. However if you are doing a trek round Europe then I would say pay more are use either legacy airlines or other LCC such as EasyJet, Air Berlin etc.

EasyJet are much more flexible about the rules. Including if you miss your flight. They will let youbook a second flight for a small fee, but with Ryan Air you have to buy a whole new ticket. Which undoubtedly will be very expensive.

If time is not at a premium then the DB NachtZug service is pretty cheap and easy to use. http://www.bahn.de The night train network is extensive and quite cheap. Otherwise there is the traditional coach service that is operated by Eurolines. http://www.eurolines.com