I know you've already accepted an answer for this question, but hands down, the best software to use is ISBoxer. It will cost you a bit of money ($15 for 3 months I believe), but even as a Keyclone/Autohotkey/HotkeyNet veteran for many years, even the most complex macros that could be written can't come close to what ISBoxer does for you out of the box.
Most notable feature is mouse repeater regions. For example, I have a region with the health bars of my party near the left side of my screen as a result I can tank and DPS with the keyboard while healing with mouse clicks that are passed from the main window (or any window, for that matter) to my healer's window. This was previously nigh impossible or impractical with the other software.
Other features include FTL (Focusless, Leaderless, Targetless setup). Previously you would have to use one of these to keep track of which was the leader character, but ISBoxer virtualizes it all for you and leaves your focus and target spots free.
If you're wondering, my group setups are 5x Paladin (1 prot, 3 ret, 1 holy) and also 4x shamans. I've 2, 3, 4, and 5 boxed for several years already. Each group size and class composition offers different challenges.
As the poster above said, dual-boxing.com is your best resource for everything related to multiboxing.