Well if your mapping stuff in XY and Z for height then you might need a 3D app. Another option is to link maps together so that when you climb a staircase then the app automatically fetches the correct next level map for you. Otherwise you will have lots of maps to deal with. A good indexing system could bypass that issue but having a good index and something to get the right one with a click is better.
In terms of linking maps together you can put them up as web pages and have links to other pages. Or you can use a map program which will do that for you too. You can use google sketchup for the quickest way to do buildings in 3D but its no good for terrain and other non city stuff. Also I don't think it can link groupings of 3D maps together. Maybe I am wrong there tho - I am no wiz at sketchup. Doing stuff in 3D is harder than 2D too.
So do you think you want linked maps or full 3D for the city ? And if linked do you think you would be organized enough to maintain a good indexing system or would you want the app to do the linking and fetching for you ?
EDIT -- ill add some more from the second post.
Most mapping apps should be able to snap to grid and not snap also. So I guess that its just an option to find. If sketching something out on paper and scanning works for you then it seems to me that its a case of organizing all those scans together into one big map. You could touch up the image with some basic flood fills or texture them a bit more or maybe go more detailed with a paint app and get that sketch looking better. So is your issue more about getting your scanned in pen work better or getting a map app that can do these things (like removing bits of wall and no snap to grid) that you want to do easier ?
It seems to me as though it depends on whether you want lots of your city mapped roughly (like pen sketch) or a small amount of city mapped really well (realistic textured etc).
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