Yes, I did the overnight train from Tashkent to Bukhara - this would have been a few years ago (2005) but I'm not sure much has changed.
Had to book the tickets at the foreigners' ticket desk in Tashkent, which had moved to an office opposite the main station, unknown to any guidebook. Booking was easy enough, but try to get some key Russian words (today, tomorrow, the names of the classes, etc).
The station itself had the standard array of snack stalls. Do bring some food and drink with you even if it's a late departure - it's a sociable thing to do to be able to share it out.
Carriages were standard ex-Soviet style, although in better condition, and with better bits and pieces (snack boxes, blankets, etc) than my experience in Russia. I opted for 2nd class (kupe), which is a 4-person lockable compartment. I'd done 3rd (platskartny) for a 35-hour journey in Russia before, and think that was an experience that was best suited to my younger years. 1st is just a posh 2nd.
The people in the carriage were incredibly friendly and chatty, despite the lack of a fluent common language (my Russian is very limited, but bits of English, French and German do strike a chord). Do share food and drink, and do accept offers to do so (you can quite easily refuse alcohol here - it is a country with a strong Muslim presence).
The ride is pretty good, and I slept well. The compartments are comfortable - decent bed space, and loads of secure luggage storage (under the bottom bunks, and over the corridor). Plenty tea available from the attendant.
Bukhara station is some distance from the city (deliberately so), and you get an array of knackered Volgas meeting you, persuading you to take them. You have little chance of figuring out the buses, or indeed of leaping on one in time, if it's anything like my visit. If you are doing the overnight in this direction, let the hotel know you're arriving early - they seem to be particularly accommodating. Alternatively, head for the ancient Turkish baths - that's quite a way to refresh yourself after a long journey!
Didn't get a chance to do the day trains, but they sound like a pretty decent ride too - especially the new Afrosiyob trains.
Both Bukhara and Samarkand are 100% worth the effort. Bukhara is like stepping back in time to when this region was the centre of the world, and the Registan in Samarkand is simply breathtaking.
Have a wonderful trip!