So we're planning Prague-Krakow-Budapest-Bratislava (day trip)-Vienna-Ljubljana-Zagreb for this Sept-Oct. There aren't really any rail passes that will seem to cover us (particularly as we plan to do the overnight sleeper cars for Prague-Krakow and Krakow-Budapest). So my question is, can rail passes be used for sleeper cars? At this point, I'm thinking just buying individual tickets sound like a better plan.
You have to pay a supplement to the rail pass for the sleeper, just as you do for seat reservations for some trains. However, trains in Eastern Europe are generally cheap. You should price-to-point tickets for your itinerary before deciding to buy a pass. For lots of info on trains, including those for the countries you list, see seat61.com