I've stayed at a couple of other short-term rentals in Prague, both on the east side of the Vltava river, near Old Town Square, but easily my favorite place to stay is Jolana's apartment in Malá Strana. It's a very busy area of town, full of tourists, during the daytime, but at night it quiets down and is a lot more peaceful than the other side of the river. There's a kitchen in the apartment, and a market downstairs, so you can prepare a good breakfast for yourself before heading out for the day. There are numerous cafes nearby, and several really great restaurants (like St. Martin, a delightful, delicious, and very economical Czech-fusion restaurant just a 5-minute walk from the apt.). It's also a very short walk to the castle complex, which we explored a couple of times, since there's so much to see. And the King Charles Bridge and Old Town are very easily accessed with a little bit of a walk.
Jolana was very kind and communicative, and the apartment was spacious and cozy at the same time, with all of the important amenities. We really don't feel like we could've done better in the whole city. Next time I'm in Prague, I will absolutely book Jolana's apartment again.