Where do you want to go? That is what I would answer first. If you want to start out in one city and fly home from another, then you have to get an open-jaw airline ticket. Otherwise, you'll have to backtrack to your arrival city.
For traveling between cities, the European rail is quite convenient (each country has their own website) as well as the discount european airlines. However, those airlines do have strict baggage limits, usually 15-20kg for checked baggage and 10kg for carry-on!!!! And they will charge you if you overpack!!!
For hotel planning, I use these websites-
www.venere.com
www.octopustravel.com
www.bookings.net
www.eurocheapo.com
Once you have decided where you want to go, I would post any questions you have in the forums at:
www.tripadvisor.com
choose the country or city and post it in that forum. eg- Rome forum, London forum, or Berlin forum........
Do not buy your train tickets/rail passes from eurail or raileurope.com, you'll be paying more than you have to as compared to point-to-point tickets or rail passes purchased in Europe.