Prague is a beautiful walking town. There are things to see - but to me it's more about walking around and taking in the feel of the place. FYI, you can do the Old Town Square, the clock and the tower in about a half hour. On my visit there last month (my 2nd visit) I spent most of my time just walking around taking pictures.

To get oriented, just walk. You can easily walk from the old town square - or start up at Wenceslas Square and walk down to the old town square first - across the Charles Bridge and up the hill (through Mala Strana aka "Little Quarter") to the castle. You can walk back across the bridge to the north of the Charles Bridge through the Jewish Quarter.

If you change your mind about a day trip, consider Kutna Hora.

We had dinner at a restaurant along the river under the Charles Bridge. There are steps going down from the bridge, and we just walked until we found a place that looked nice.

We also booked a local walking tour of Old Town and the Castle area. The guide was good and gave us a lot of historical information.

You say you don't want to day trip, but we went to Cesky Krumlov and really enjoyed it.

In Vienna, we saw a performance of the Lippizaner horses that was superb--and I'm not an animal lover. Also went to the Summer Palace and ate lunch at the Gloriette on top of the big hill behind it. Worth the walk up! If you are a dessert lover, Vienna is heaven.

I was just at Vienna and I decided whether to take CAT or S7 depending on which train was leaving next. There were CAT ticket machines in the Vienna airport luggage carousel area, but I noticed it was 1:35pm, and I would have just missed the 1:35pm CAT, so I took the 1:48pm S7 instead. It took 10min from the luggage retrieval to walking to the OBB station, buying tickets (takes bills), and be on the S7 platform direction Floridsdorf. It was Saturday and the train was not crowded at all to the Mitte station.

Are you planning to visit the Upper Belvedere Palace on the arrival day? The garden is pretty large going up to the palace, but I did not think it was a stunning type of garden. The highlight of my visit were the Klimt collections at the Upper Belvedere Palace, but it may not be a good arrival day activity.

You have 2.5 days in Vienna and 3.5 days in Prague and don't want to take a day trip? Pity, if it were 3.5 days in Vienna and 2.5 days in Prague, you could have taking an easy day trip to the Schönbrunn Palace mentioned above just outside Vienna.

In Prague you might want to walk down the Wenceslas Square starting from the National Museum (which has elevated entry from which you can see the Wenceslas Square) all the way up to the Old Town square. Notice beautiful baroque buildings like Hotel Europa. You want to wear shoes with hard soles and good ankle support in Prague. The cobble stone streets are killer for soft sole shoes.

I agree with Greg about shoes in Prague. I tweaked an ankle falling off a cobblestone last year. You mentioned wanting an Italian restaurant and we found Palatina at the Hotel Leonardo. it was very good.
My trip report on Prague from last year is here: http://www.fodors.com/community/europe/prague-trip-report-173546-2.cfm

Thanks everyone! I appreciate it!

Prague is a beauty and just walking around looking at the architecture and facade embellishments is interesting.

If you like museums the Mucha Museum is fascinating and small. I enjoyed the Municipal House tour. While walking down from the castle area be sure to see Nerudova Street with the interesting signs above the doorway and the wonderful building facades.

You haven't mentioned churches but in case you like to visit church be sure to see Tyn church (on Old Town Square) and St. Nicholas church (the one going toward the castle, not the one in Old Town).

I haven't done this but there is a mirror maze on Petrin Hill that might be interesting.

I ate at Kolkovna restaurant one night; it's between Old Town and the Jewish Quarter. It's moderately priced and was very busy so it's popular. I can eat very good Italian food any time so I wanted Czech type food while I was there.

When you have some free time in Prague, I suggest to go on Petrin Hill and visit Petrin´s Observation Tower. There is an amazing view of Prague castle and Lesser town. It´s a nice walk. You can take a funicular from Ujezd to get up the hill.
Ambiente Pizza Nouva at Revolucni str. is a very good italian restaurant.

for czech-style food, the restaurant in the basement of the Municipal Hall is very good, and not expensive; they hold concerts upstairs in the concert hall on occasion.

Have to agree with BaraPraue

Use your free time to walk up Petrin Hill, The Fall colours should be nice now, though Petrin Hill is nice anytime.

1.Walk along the Hunger Wall.

2.Walk to the Observatory to see the Rose Garden

3.You will be passing the Way of The Cross as you ascend near the Petrin Tower.

4. You will come across a very lovely monument to Karel Hynek Macha , a romatic poet writer who died at the young age of 26.
it really is quite a lovely statue to him.

5. By the Petrin Hill Tower you will see the Church
of St.Lawrence and the Calvary Chapel besdie it.

You will get nice view from the top looking down on these buildings

6. There is a small fee to climb the tower.
You can climb half way up, take a few pictures and then continue on to the top.

Now you are at the top..... terrific view over Little Town and Old Town Prague..... get the camera out !!

Oh yes... if you do not want to climb up the hill, there is a funicular,

but I recommmend walking, it is a switchback road going up, so you are sort of zig-zagging back and forth.

You see more walking up !

Finally I would go to Petrin Hill by walking over the Legions Bridge

becasue this way you will see the Monuments to the Victims of Communism

<<We had dinner at a restaurant along the river under the Charles Bridge. There are steps going down from the bridge, and we just walked until we found a place that looked nice.>>

What Carolyn is describing is KAMPA ISLAND.

As for restaurants in Vienna and Prague you can use http://www.comfortway.com/ to book tables there online without need to call to the restaurant, there are descriptions of restaurants.
I used this website and their app when I was in Vienna.