My friends and I cycled from Vienna to Budapest. I used the Cycline Danube Bike Trail (section 3) guide which is great as there are few signs, I was giving directions to other cyclists along the way. If you cannot find the German version (Bikeline) also works as the maps are good. Danube Cycleway written by a witty Englishman is also helpful.
Vienna to Slovakian border - no maps needed as route in Austria clearly marked, you must get off bike path at the border to cross for a few feet as bike path starts again almost immediately.
Slovakia - bike path passing Bratislava, clearly marked the entire distance to Hungarian border.
Hungary - need maps as route is unclear at times particularly around Gyor and entering Esztergom. Local people do point out the correct directions even though they do not speak English. Route splits, best and most scenic is the inland route via Gyor.

Tom