Gray Line tours does a number of tours and if you google "London day trip tours" or something, you'll see a lot of companies that will be happy to take you wherever you want to go. As others said, I would highly recommend the train system. Its easy. The ticket agents are helpful. Basically, buy a guidebook that includes the places you want to go and tells you the train station that train departs from. That's really the only tricky part. The train depots are conveniently located near what you'd want to see and well within walking distance.
I'd definitely do Stonehenge if you haven't already, but also Hampton Court (great maze and grounds), Leeds Castle or Warwick Castle if you have kids...they're pretty touristy, but fun for young children...York if you have time...Stratford-upon-Avon and Dover are both fun and educational sites...ah, England...so much to do! Windsor castle is easy and quick to get to. There is also an amusement park called Legoland Windsor out that way, so if you have kids that are tired of musty old buildings, that could be something fun. Blenheim Palace is fun (and you'll recognize it from movies and TV). Salisbury Cathedral. Canterbury. There are literally loads of options.