Come stay with Bonny and Max! They are very good at taking care of their guests. I was at a conference in Prague and needed a quiet place to retreat to (and finish a paper) and this was perfect. It is opposite to a kitchen that serves delicious Czech food and in an area with a lot of bars and cafes (with live music). It is extremely well connected in terms of getting to the Faculty of the Arts of the Charles University (basically door to door) and is close to the 58 tram (which runs at night).
The room has everything you might need for a short stay, a very good coffee machine, and double blinds in case you want to sleep in (and there were no mosquitos, a real plus in the summer). Bed is a fold-out that actually is remarkably sturdy and comfortable (and can be used as a couch during day). There is also a 24hr shop on the corner of the block.