These are great questions.
First, we (Toni, Rob, Dee and I) don't do buses and since private tours are usually no more than ship tours, we booked all private tours. I booked a few, Dee booked most, I dealt with cruise bookings, air travel (for Dee and me) and some ground transportation.
Darlene used Viator a lot as it consolidated everything in one place, though it is more expensive for the guides has good reviews and protections. Tours by Locals was used for some as well. I'd recommend any of our guides.
We were not worried about paying for, or doing deposits in advance, as using credit cards comes with quite a bit of protection and we would not book with a guide who would not offer a written refund policy if we couldn't make the port.
Here is a summary of tours and guides.
Frank Law, Ancient Chinese Budist temple, Victoria Point by the cable car, Stanley Market and park for lunch (we missed Aberdeen due to traffic). We used a guide recommended by the hotel for Lantau island and she was GREAT, but I'd have to find her name since she was a last minute addition she was never on our spreadsheet. You may be able to do this on your own. We also visited some sites on our own like the ladies market, some shopping, Macau, etc.
Indo China Junk reserved through Best Price VN You can also book direct and would DEFINITELY recommend splurging on a private, overnight trip. Most of the boats seem pretty similar, we LOVED our "Prince" Please note, boarding is at noon.
Da Nang / Hoi Ann Best Price VN again and had a guide named Lucky. This was probably the least luxurious vehicle and had almost no suspension. He also waited outside the port gate, which caused a bit of a walk, even though we thought he would be inside. The same thing happened with our ride in Halong Bay, so if you use Best Price VN, make sure they pay whatever fee to come pick you up at the ship. The tour was an ecco tour with cycling through the rice paddies and a local lunch, but it was highly modified as we went, again an advantage of a private tour.
In Saigon we joined up with fellow Cruise Critic roll Call members for a city tour of Saigon. Again we had to walk out of the port 200-300 meters (yards) but had a great tour with a good guide who took us to tourist spots AND back roads in Ho Chi Min (read Alleys) to show us local life. He also took us to the old CIA building where the last American's were evacuated, and I believe is the only guide who can do this. Check out our Roll Call to find Kevin's contact info.
Bangkok Nat at Your Thai Guide. She has a number of guides (7 I think) who work for her, and was a great guide. Tell her the princesses sent you
We did an overnight in Bangkok and she went with the flow, adjusted the schedule and tour as we needed and stayed with us from Pick-up at the port through the night (dinner). She took us to local restaurants, and lots of local sites besides the main tourists sites. She was the most expensive guide but everyone thought it was worth it. I still think we spent less than a ship's tour. As I said before, I don't know if I can recommend our hotel due to the less than ideal location for tourism.
Singapore Anna Ong through Viator and she was great. We did public transportation the first day, which was not ideal for us, but mid day she was going to get a car when we asked, but instead she suggested a way to change the tour, eliminate walking and make the best. She had a car for us the next day, and had a great local lunch, in a local HBD appartment.
I booked a private boat through Jet Set Travel, more expensive than most tours in Bali, but reasonable compared to many locations, and again, private
Giri Putera*Wayan was our guide for the other day of touring was GREAT, and very inexpensive.
We were set-up on a private tour in Komodo with other Roll Call members, but as you know, this never happened
Phuket Patthanant Ketkaew through Viator, we did an Elephant "Trek" though I am not sure I would recommend this, probably better to do it in Northern Cambodia where Elephants are native and they have more water to care for them. We also toured the city, beaches, etc She has a GREAT secret lunch spot, and reminded me a lot of Nat.
Langwaki We used Farly. Our guide is no longer guiding full time and now lives on Penang so we had to cover the cost of his hotel and ferry (it was built into the cost) which again, was pretty pricey in my estimation, BUT when we compared what we got, compared to our friend with a ship tour, it was very, very comparable. We did an island and boat tour, some shoppinga and he included all entrance costs, took us to our MOST local meal, flies and all, and again totally custom tailored the tour, including stopping the boat for us when we wanted to go to a beach for a swim.
Kuala Lumpur Diana*Lee Geok-Chin again through Viator, but these guides are probably easier to find on tours by locals. This was kept pretty mellow and short on purpose, as it was our last day, just a couple of stops and lunch and some drive byes, leaving a reason to come back to this up and coming city.