Just got back from Lebanon a few days ago. My itinerary was very simple:
Day 1: arriving Beirut at 2.35 AM, just wandering around Beirut center
Day 2: day tour to Baalbek, Anjar and Ksara winery, with Nakhal Tours
Day 3: Qadisha Valley, guided hike tour, with Living Lebanon
Day 4: Byblos, with public transport
Day 5: Tyre, with public transport
Day 6: flight back at 4.05 AM
I would have wanted two to three days more to cover all the places I wanted but at that point there were not chances for longer trip. And didn't want to rush from place to place. So there were not any TWHS visits as I originally planned.
I stayed at Beverly Hotel
which is quite nice hotel with very good location. The only disadvantage was that there were some problems with hot water in my room.Visiting WHS (without rental car)
Baalbek and Anjar are reasonable to combine to a day trip. There are lots of offerings for Baalbek and Anjar day tours which always include Ksara winery visit. While the Nakhal Tours day tour was quite well organised, I don't recommend these day tours. In my opinion there are not enough time to spend especially in Baalbek which needs minimum two hours. We had only over an hour at Baalbek and some half an hour at Anjar. With my current knowledge I recommend spending a night in Zahlé and having a taxi from there to both sites.
While I little bit regret my day tour to Baalbek and Anjar, I enjoyed my guided hike at Qadisha Valley. In my opinion the best way to experience Qadisha Valley is by hiking. That is because of the great views and because many monasteries and churches could be visited only by foot. We visited 3/4 of the main monasteries of the Valley and one church. Of course the same route could be done without a guide but there are not that many signs along the path network so finding your way could be difficult.
Byblos and Tyre are best and easiest visited by public transport. Take a bus for Byblos from Charles Helou bus station. It takes 45 minutes to an hour depending on traffic. The only difficult thing is finding an entrance to the Charles Helou bus station which is crammed under the road bridge. For Tyre take a taxi to Cola intersection and jump to one of many minivans. Contrary to what many guidebooks tell, the trip takes only one hour.Safety
For anyone who hesitate visiting Lebanon for safety reasons, don't hesitate. I didn't feel unsafe or any kind of threat. In Beirut I felt safe even during late evenings. Of course I wouldn't want to spend too much time in Bekaa Valley area near Baalbek. There were lots of military checkpoints and Hezbollah hegemony.
The only place I felt a bit unpleasant was Tyre around Al Bass roundabout where minivans from Beirut arrive. There were lots of serious looking men that stared me intensively and sometimes shouted at me. After visiting nearby Al Bass archaeological site I tried to take a shortcut to Al Mina archaeological site but soldiers stopped me. They said that Americans or Europeans are not allowed to pass the street. I thought that it was because of numerous Hezbollah flags along the street, but later I realized that it was because of Palestinian refugee camp located just beside WHS. But as soon as you get to the christian quarters near the old port, the atmosphere is much more relaxed and friendly as it usually is in Lebanon.