Based on a day trip to Bratislava in 2007.
Bratislava cannot rival Prague or Budapest, but it does make a very nice day trip from Vienna, particularly if you go by boat along the Danube. Bratislava has a small but pretty pedestrian old town with cobbled stone lanes and lots of cafés, an interesting shopping street and some nice avenues along the Danube. For a good view of the old town, head up St Michael's tower, one of the gateways to the old town. For a more extensive view of the surroundings (dominated by an immense stretch of communist-style housing estates), you can also walk up to the castle (which is a modern remake without any specific attractions).
Boat trips from and to Vienna are rather pricy, but worth it. The boat trip is almost as fast as the train and it will get you right to the old town (while the train station is quite a walk from the old town). Also, going by boat along the Danube is a great way to experience the Donau Auen Nationalpark with its amazing floodplains and trees. Taking a boat back to Vienna in the late afternoon is particularly nice, as you will be riding towards the sunset and get impressions like white herons flying against red clouds... If you preplan your boat trip a little, you can save some money by taking the cheaper boat company LOD which offers good round trip fares. Twin City Liner boats are more expensive. Also, call ahead as boats are often fully booked.
Useful links:
Bratislava Tourist Service
Lonely Planet Bratislava
Rough Guide Bratislava