Robert,
I use TC2000 Platinum and Telechart 2007 Platinum from Worden.com. TC2000 is actually an advanced subscriber version of www.freestockcharts.com where you can do the exact same tasks for free, but with delayed intraday data and only from the BATS exchange.
All annotations are made by hand. Many EV members have offered their help for automating the charting process, but I have vigorously refused any automation on my side. It is the most important step of my daily routine, as updating manually allows me to note even the slightest details changes. On the weekend I often spend 2 or 3 hours just meditating on the clusters structures for IWM, SPY, QQQ and GDX, mentally visualizing all scenarios for the following week and anticipating the best trading plan for each case. Doing it manually helps me memorizing the dynamics at work because I have an excellent memory of everything practical I am doing.
Billy