Having followed all of the great advice on this forum, I thought I would share our experience of our trip to Neuschwanstein.
We pre-booked our tickets online which I would definately recommend. The queue for non-reservations was huge and we simply walked to the front of the separate reservations entrance which had no queue at all. The extra couple of Euros to reserve your tickets is well worth it!
We caught the train from the HBF direct to Fussen. As we were travelling on a Sunday, there were no restrictions on the times we could travel and so we bought the bayern ticket at the ticket window which was really straightforward - 28 Euros I think and we were told what platform we needed. The train takes about 2 hours and ends at Fussen. We then caught the bus from directly outside the Station up to the Hoschwangau (bayern ticket also covers the bus).
From the drop off point, its a couple of mins walk up to the ticket office. We collected our tickets and as the shuttle bus wasn't running during our visit we walked up to the castle. It is quite steep but is fine at a steady pace(and you don't need walking shows unless you follow one of the trails off the main path). It took us about 25mins to reach the castle. We then walked up to Marienbrucke (another 15mins) - which is where the shuttle bus would normally drop people off - in order to view the castle from the bridge. Note that the bridge is not good for people who are afraid of heights! However, the views of the castle from here are amazing and I would thoroughly recommend making sure that you get to the bridge.
Note that there is a small bit of scaffolding on the castle but it isn't really noticable and certainly doesn't tarnish the overall stunning views or your photos. I think that the scaffolding is being done in small chunks and won't be finished until sometime in 2011.
It was then time for our allocated tour. You need to wait in the courtyard of the castle entrance. Your ticket has a number on it and once it comes up on the screen, you put it into the ticket machine and go into the castle. Make sure that you are there on time, otherwise you will miss your slot. The castle is very ornate and beautiful inside, although you can't take any pictures of the interior. You are only allowed to take pictures of the views from the windows. There are great views of Marienbrucke from inside the courtyard too. The tour lasts around 30min and there were about 25 people on our tour. You don't get long to ponder in each room as there are other tours both in front and behind you.
We then had some lunch and waited for the bus to take us back to the train station. However, the bus was late and we thought that we would miss the train. However, luckily, they held the train at the station until the bus had arrived. The train was very busy, although we did manage to get a seat. On the way back, we had to change in Buchloe which is really easy. Basically you get off one train and then get on another from the platform opposite.
Given the high costs of arranged tours to Neuschwanstein, I really don't think that its worth the extra cost. It is really easy to get there by train and would fully advocate travelling there independently.
We really enjoyed our trip and thought it was truely a fairy tale castle. Would definately recommend a trip out there if you have the time.