looking for comments on my backpacking trip

The first thing that pops up is that you've allotted about the same number of days to each spot, probably not with much thought about what you actually want to see or do in the places. It's just Xs on a calendar with some travel times. Rather hard to comment upon without knowing what rings your bell. Cinque Terre is what, a lunch stop on a non-day?

Just trying to see as much as possible in the days that we are in each city, do you think I should get rid of one or two? I never know if i will make it back so I want to do as much as possible. Also Cinque Terre, I am thinking about 1 over night and 2 full days to hike the 5 cities.

I think you are visiting too many cities and not enough smaller towns/countryside. Overall, I would cut Brussels, take a day off Prague and go to Salzburg instead of Munich. You could make a day trip to Munich from Salzburg. There are many lovely day trips from Salzburg into the mountain which might make you forget Interlaken altogether. Look at your routes for interesting towns/countryside you will pass, such as Cesky Krumlov. I would also add a day to Rome.

I concur with Emily; this is an overly-ambitious itinerary for the amount of travel days you have available. Also, don't discount the impact of jet-lag for your first couple of days. I would drop Brussels completely and cut a day from Berlin to start. I think 3 days in Rome is a bit much, too. But everything is personal preference. If you like the outdoors, I would add another day in Interlaken/Gimmelwald, but be flexible enough that if the weather doesn't cooperate you can move on or if you have unanticipated delays you can adapt your schedule accordingly. Personally, I like Munich, and have found it to be a flexible jumping-off location if the weather doesn't cooperate. In October 2010, I spent several weeks traveling in Europe. I flew into Brussels and spent 2 days there (which was two too many). Train to Amsterdam for 3 days (perfect). Train to Nuremburg for 2 days (would probably skip if could do it over again) followed by a bus to Prague for 2 days. Train from Prague to Munich for 3 days, including a day trip to Fussen. Train from Munich to Gimmelwald for 3 days (FANTASTIC and weather was perfect). Train to Bern for a night (skippable) and final night in Zurich (also skippable, but was interesting in it's own way). Train from Zurich to Brussels to catch flight home. I flew in from the Middle East, so jet-lag wasn't an issue, but depending upon where you are traveling from it could be...

It's a good survey trip if you really think you won't ever get back. You might be heavy on Brussels. I like it, but if I had to drop anything, it'd be Brussels. Switzerland is expensive and especially the Jungfrau/Eiger train. If you time it right, you can take the first/cheaper train up, fiddle around, come back down, then go ride the lift to First in the afternoon and be back in the hotel for supper. That cuts it to two nights in Switzerland. The whole CT trail system is only six or seven miles long. You can double- walk it in one day with a beer/coffee in each village. If you hadn't been influenced by Mr Steves, it wouldn't even be on your list. For a survey trip, you've skipped Paris. You could stick it in in lieu of Brussels and add the day saved in Switzerland. You must have something special in mind for Munich since it's nowhere near the same tier as the other places. You're over-citied. Pick a small town/village at about the midpoint and sit on your butt for a night or two. Take a day out of Amsterdam and give it to London, the apportionment of time to sights is all wrong. I like Amsterdam so much that I ran in for lunch on a layover the other day, but there's just too much to see in London for the time you've given it.

If you haven't already purchased your train tickets (train?) this will be an expensive trip. Since you're posting your itinerary, I assume you haven't . Having a railpass won't be your savior, for the most part, either. I think Munich is distinctively different from your other locales; 2 days isn't too many. What are you planning for Brussels? While you can fill 2 days there, you might prefer somewhere else (Bruges, etc.). I'd also suggest dropping the CT for this trip. For someone who lives in NY...you can get back to Europe waaay easier than most of us can, and for faaar less money too. See the CT later. Be prepared that you may not get to the Jungfrau. Well, you may not see it. I'd never suggest not trying to, though, so you'll want a couple of days to get a good weather window.