My day trips thus far:
From Vienna I did the Melk Abbey by train-boat along Danube to Krems-train back to Vienna and that was a great day of exploring. Another long day trip by train to Salzburg (worth much more than a day but that's all I had) arriving at 9:30 am and back to Vienna by 9 pm.
From Budapest I've taken the HEV twice now to Szentendre--very pretty little town along the Danube and I like to have a late lunch at one of their restaurants and explore the shops, plus if you go on a Friday there's a craft/handmade item and food fair going on in the main street. HEV to Godollo--great palace/museum to visit and lovely little town. I also visited the town of my ancestors, 1 hour by train to Tata--I would need a car to see some of the further outlying sites there.
Next trip will likely include a day or two in Debrecen, near the Ukrainian border, and Pecs, and a day trip to Bratislava.