However, while researching Vienna I didn't see much of anything that I felt like I must see. I have heard good things about Vienna and it seems to be pretty popular with the users here so I think maybe I'm missing something... What did you (or anyone else) do while in Vienna? And what would you recommend? Thanks!
Vienna is a popular choice at GFE, and as I've said, I'd recommend it over Nuremberg, however you need to know what would be of more interest to you.
To add to the suggestions from the new Vienna Tourist Board (aka
herrbert 
), more things you can see/do/eat in Vienna are:
1. visit the Hofburg as well as Schönbrunn Palace - both are spectacular and not boring at all as there are far too many pretty shiny things to drool over (the Kings Appartments, the Silver Room)! Maybe an audioguide will be better than a guided tour as you can move at your own pace. The Hofburg is in the city (the Winter Residence) and Schönbrunn is about 15mins by U-Bahn from the centre (the Summer Residence) so you can do both in a day or just pick one (my choice is Schönbrunn) if you're short on time.
2. visit the Kaisergruft (or Kapuzinergruft at Tegetthoffstr. 2, two blocks behind the Opera towards St Stephans, just past the Memorial Against War and Facism), last resting place of the bodies of the Habsburgs; only their tombs are visible, so not too grim, but interesting nonetheless. Their hearts are kept in St Augustin church around the corner, but you need to pre-arrange a visit to see those.
3. St Stephansdom - I love the roof of this cathedral as it looks like trippy 70s wallpaper! Take a tour of the crypt (catacombes) under St Stephan's Cathedral; there are short guided tours of this rather interesting part of the church. The crypt is where 11,000 people were buried until the late 1800s, when burials inside city walls were banned, and victims of the plague were buried via a shute leading into the basement. You can also climb the 343 steps of the north tower for great views out over the city.
4. Bakery tour - do what the Austrians (and Germans) to and at 4pm have "Kaffee und Kuchen" (coffee and cake). Grab a strudel, Sachertorte or whatever takes your fancy at
Cafe Hawelka (Dorotheagasse 6) which is a Viennese classic coffee house, try the coffee at
Demel (at 14 Kohlmarkt), sit down in the
gorgeous cafe on St Stephansplatz next to the church (can never remember the name but it overlooks the square), or try
Cafe Diglas (Wollzeile 10, near Stephansplatz) and enjoy a strong Austrian coffee (Kaisermelange is with milk if you don't like your spoon standing up in your coffee!).
5. Spanische Reitschule/Lipizzaner riding school nad the Vienna Boys Choir - if either of these things ring any bells or sound like something you'd enjoy the look them up on the relevant websites:
www.spanische-reitschule.com/ and plug in the dates you'll be in Vienna to see what going on in terms of performances or tours (they take a break for part of Summer). If you're there for morning practise, grab tickets. The musuem attached isn't half as good as seeing the real thing in action. The Vienna Boys Choir (Wiener Sängerknaben) performs in the Palace Chapel (Burgkapelle) for Sunday Mass, and this beautiful church has free standing-only tickets for these performances from 8.30am. The Choir performs at various times throughout the year, however goes on tour in Summer (around July) so check
www.wsk.at for the dates.
6. Judenplatz (Jewish Square) - “The Nameless Library” and other exhibits located at the country’s first memorial to its Jewish heritage; built on the site of an ancient synagogue in the centre of the Jewish Quarter around Ruprechts Kirche and Judenplatz. The Jewish Museum is located on Dorotheegasse in the center of town.
7. If the weather is good, spend time in one of the parks (Stadtpark is a good choice) munching on a picnic (there's that bakery theme again!) and watching the world go by.
8. For something unique, visit the Opera Toilet located in the U-Bahn under the Opera House. Pay your entry fee (about 60 cents) and listen to Mozart’s music while you do your thing!!!
Cafes & Restaurantsherrbert and I often disagree about schnitzel places in Vienna - I've always enjoyed
Figlmüller and he prefers
Restaurant Gutenburg - both are good and the schnitzels are huge, crunchy and tastey, so in the interest of neutrality, you choose whichever one you think you'll enjoy ;D There are great Heuriger (farm-house taverns serving their own wine) in the hills of Grinzing and Gumpoldskirchen outside Vienna, but they take over an hour to get to, so stick to the city this time around.
Café Restaurant Landtmann (Dr-Karl-Lueger-Ring 4) where Freud reportedly took his morning coffee in this old-style Viennese cafe.
Restaurant Beisl is an old Jewish restaurant and Vienna favourite.
Drei Husaren (Weihburggasse 4) or
Plachutta (Wollzeile 38) both have good Austro-Hungarian food and a specialty of Tafelspitz (broiled beef with apple and horseradish sauce).
Sacher Hotel - If you really want to spoil yourself, go the whole hog at Cafe Sacher and have Sachertorte with cream and strawberries. This is the home of Sachertorte, and it's kind of cool to have it there, but good Sachetorte can be found around the city if you don't feel like blowing your budget on the original.
There are some great places to eat at
Prater too: beer halls, food stands, etc, and you'll find they aren't that expensive either.
Just a few notes on your other destinations:
Brussels - great city, I'm a fan, but you may find that you need only 1 full day here (make sure you choose the day all of the museums are open - ie not Monday) and at least 1 full day in Brugge as well as a day to visit Aachen (unless you want to overnight there, which will change your itinerary a little)
Switzerland - if you're into scenery, look into the Berner Oberland, places like Lauterbrunnen, Gimmelwald and Interlaken, or the bigger city of Luzern. Geneva is really not that exciting in terms of scenery, the mountains around it have better towns, ditto for Lausanne. Bern is very pretty, but small enough to cover in 2 days. I'd suggest dropping Lausanne or Geneva for Luzern or somewhere in the Berner Oberland. If you want to be right in the mountains, then this is your region.
), more things you can see/do/eat in Vienna are: