Lol... We attempted to do a similar thing last summer... the whole of europe in 6 weeks... its a tough one! If you're going for a year you have slightly more time but there are definate musts on that list!
Firstly i would recomend an interrail pass, it allows free train travel in all EU countries, train is absolutely the right way to travel. secondly i would recommend "Europe by rail" its a book designed for people backpacking europe by rail on a budget and will be perfect for what you guys are doing, it has scenic routes marked out and links some of the top places together in routes so you can relax a bit - you can also get a european train time table which has pretty much all the train times for the entire continent. We did it without but it would have been useful to say the least!
I would start in France, do paris and work your way down depending on how much time you have... you could spend a little time in the loire valley or where ever takes your fancy... you could stop off in barcelona and then work your way down the south coast and through the riveira. I would definately recomend Nice, it has a lot to do, lovely weather and great beaches. Monaco is also worth a day or 2 although you probably wont be able to afford to stay there. but its certainly worth while... my boyfriend wanted to go just to look at the grand prix track, but the casino is worth going to and to look at the jaw droppingly priced jewellery in the shops next door!
From there I would either venture up into switzerland (Bern is lovely) or down into Italy... Obviously Rome is a great place to start, Naples is beautiful with great pizza and a real italian atmosphere.. You can climb mount vesuvius, go to pompeii (for which i would recommend a tour guide) or herculaneum and definately check out sorrento and the amalfi coast which is beautiful.
Venice is great, and on the 3rd weekend in july they have a huge festival with fireworks and a party on the beach til the wee hours.. i think its called festa del redentore but if you can get to venice for then i would!
austria - in salzburg they are obsessed with the sound of music, the YoHo hostel does free showings every day! but its a beautiful city, i would visit the castle and perhaps to helbrunn with trick fountains by bike (if you can get a tour do - we got totally lost for several hours!!) Halstatt is a tiny little village reached by a boat, its quite touristy but unbelievably picturesque. they have the worlds oldest still mined salt mines which you reach by train and sliding along on wooden slides on your bum! Vienna was also one of my favourite places, it has a film festival in the summer which is great if you can fit it in.
Slovenia- Llubljana is wonderful, it has so much history and there are some fantastic museums. its got a real sense of national pride - there are lots of places to drink aswell! visit lake bled on the way out, its amazing, i think you can hire boats in the summer and ice skate in winter or just walk around the edge.
Krakow is amazing, and very cheap, you can visit auchwitz for the day which is shocking but very interesting, free with an interrail pass. i think thats free entry but 12 euros for a guided tour and movie which is worth it.
Germany - munich is amazing, oktoberfest im told is fantastic and well worth going to, but the city itself is fantastic. Berlin to is brilliant and you can get free bike tours from sandemans tours.
Prague i would go to, go and see the astrological clock when it puts on its "show" on the hour. you can get free walking tours here aswell, look for leaflets but they meet outside the tourist office at 9am every day but sunday if i remember rightly.
I wouldnt recomend scandanavia unless you have a large budget and dont mind rain... although my experience may bias me slightly!
Have a great time and i hope this helps!