Kutna Hora is a great day trip to do on your own, the link above shows my contributions about the town on trip Adivsor.I was last there in November last year with some American friends.Easy to do on your own but there is a bit of walking about.
Karlstejn castle is also easy to do on your own but is really only a half day trip but when I go there I usually do a bit of walking in the area and have in the past walk from there over to Beroun but it is about 5 hours walking.
Never been to krivolat but that could be included with Karlstejn but you would need to check transport ;links.
Konopiste is a nice place and close to Benesov again not a full day so worth considering.
I will throw in one of my favourite place Tabor a hussite town about 90 minutes by train from Prague and a great place for a day trip , small but very interesting old town with enough to keep you busy for a day trip.
This is an excerpt from my trip report there a few years ago.
We have a day trip to Tabor today. I had heard about this place on travel forums and found out that it was easy to get to from Prague, Andy had some DVD’s of European train travel and Tabor was featured in the Czech Republic one so we decide to go.
Return tickets cost 382kc for the two of us and we left from Hlavni at 9.16 am, the journey was fine until we reach Benesov where we have to transfer to a bus as there is some engineering work being done to the track, about 30 minutes on the bus took us to some place that shall forever remain nameless, a 2 horse town in the middle of nowhere, we re join the train and are in Tabor about 10 minutes later than scheduled.
Once in Tabor we walked to the main town it is a 10minute or so walk but there are buses you can use, we enjoyed the walk and were delighted by the small town of Tabor, it has a warren of streets that are quite confusing, for many years this was an enclave of the Hussites in the Czech Republic and they basically rebuilt the town, I am not going to give a history lesson, you want info just google it.
The place is really nice with a town square some obvious town walls and a very nice little tower which gives great views over the town and of the surrounding countryside. There is also a medieval museum within the tower building which is very nice and informative, cost for both tower and museum was 80kc each.
We have lunch in the restaurant Modra Ruze, pork steaks with ham, potatoes and loads of veg. (150kc); it was very nice though I wasn’t so keen on the potatoes. this was washed down a Staropramen beer (22kc).
Fed and watered we headed to the town hall and to the Hussite museum there, nice exhibits and some great dioramas of battles ,all a bit lost on me as I just could not really work out all the history.
We then took the tour of the underground vaults that start here, The Museum and vaults tour cost 100kc for both.
The tour was great fun, you have to wear a hard hat and even someone as short as me bumps their head, we joined a tour with about 40 school kids and their teachers, the tour was in Czech and we were the only 2 non Czechs on the tour, the guide very kindly came to us at each interesting bit and explained in basic English where we were so we could check on the English crib sheets we had been given ,very kind of her it was not in her remit to do that but she kindly gave us that info. The tour finishes in another part of the square and we return the short distance to the town hall to return our hard hats and crib sheets, it has been real fun. We then take a wander out of the old part of town and down to a waterfall area and carp farm, all very nice though the waterfall is a bit quiet, we then walked along the man made reservoir (there is history about why this was built, something to do with a fire in the old town and no water to put it out) back to the station.