I know that many people will scoff at this, but we were very satisfied when we did this in Paris and London, as it allowed us to get a good overview of each city and determine which sites we wanted to explore in greater detail. The other issue is that I am somewhat limited mobility, an all day walking tour is not an option for me. Anyone have experience with this in any of these cities? Thanks!

Can't help with Budapest or Vienna but this is the info fror Prague HOHO bus.
http://www.prague-information.eu/825
To be honest with you the HOHO bus is really not a great option in Prague,the majority of the tourist areas are pedestrianised and the buses can't get access to all the sites and basically drop you off nearby and you have to walk.The HOHO bus really does no more that what the public transport system can do ,so I would usae the Trams and metro (24hr ticket 110kc) and use that.
http://www.prague.net/itineraries-in-prague
this website has lots of great info including Itinaries and you could follow these at your own pace doing what you can when you can,there are loads of cafes,bars and resturants where you can stop for a rest as well as numerous other places you can take a breather at.
http://www.dpp.cz/en/
this is the public transport wesite ,again lots of info including transport maps,and matbe you can try and plan your trip using the info on the websites provided.
Sorry I can't be more positive but Prague really is a walking City but with a bit of forward planning and use of the excellent public transport system you should be able to manage to see many of the wonderful sights.

Thanks!

you're welcome

Bookmarking for the Prague itineraries, Thank you .

a little update on HOHO in Prague.
http://www.livingprague.com/tours.htm
this link will link you to a HOHO tour in Prague as well as many other.
I was having lunch with the person that runs this website (Jason) last friday and he was telling me there is going to be another HOHO starting in Prague and was going to a meeting about it this week, hopefully the website will be updated once he has all the info.
I was in Prague last week on and of a few times and did see the HOHO buses , they are small mini bus type things and did not seem that busy, very different from the HOHO buses you see in other major cities.

I did a hop on hop off in Budapest. There are several companies that offer it.
I can relate to someone with mobility problems. This was the first time I did a tour like this and the only reason I did was that my traveling companion always does them.
What I would suggest to you is that you really research the stops that you would like to see because you should skip those you are not really interested in.
The reason I say this is because I didn't think the time allowed was really enough time to do all of the stops justice.
For instance, we spent a lot of time on castle hill.
This is a great way for you to get an overview and to limit your walking.

P.S. The company we used included a coupon book with discounts for several things. One was a free boat ride along the Danube and I really enjoyed this ride. It was a beartiful day in October. I think this was the only coupon that I used from the book but there are lots included which may interest you.
And it a great way to get an overview of some of the historic buildings that you may not otherwise be able to walk to.