Favorite Day trips from Prague?

Favorite day trips from Prague for me: Castles Karlstejn and Krivoklat. To do both at the same day would be rushed. Chateau Konopiste. Town of Kutna Hora. Information about these destinations are in Rick Steves book: Prague & the Czech Republic.

Its only 3 hours to Cesky Krumlov so you could leave very early in the morning and spend a day returning very late in the evening as its well worth a visit but for no more than a day.

I've always heard great things about Cesky Budejovice but I haven't been there myself...

Ceske Budejovice and Cesky Krumlov are certainly towns worth visiting but as a day trip from Prague would be too rushed. If you could stay overnight I would recommend both. Cesky Krumlov is well described in Rick Steves book Prague & the Czech Republic. In Ceske Budejovice you can walk the old historical town, visit and have a tour of original Budweiser brewery (german name for Ceske Budejovice is Budweis), go to nearby chateau Hluboka or (and) visit well preserved south bohemian village Holasovice (it's in UNESCO heritage list).

Thank you for your great suggestions! Are there good ways to get to any of these places via public transportation?

Yes, you can get almost everywhere in the Czech Republic by public transportation. To Karlstejn and Krivoklat by train, to Konopiste by train to Benesov then walk or taxi. Maybe there is even local bus, I don't know. To Ceske Budejovice by train or bus (about the same time). If you want to continue to Cesky Krumlov by train you have to change trains in Ceske Budejovice. Or you go from Prague by bus direct. Once you get to Prague you can get your tickets to wherever you decide to go.