Well, i just subscribed to ISBoxer so i thought i'd post a little debrief about keyclone and ISBoxer.
This is obviously just my understanding/experience (please correct me if i misunderstood some things), but i think some new people could find it useful.
This is all based from a World of warcraft point of view

Although the overall goal of those two softs is the same (sending keystrokes and mouse events across multiple game instances, managing screen position etc) the way they approach it is quite different.

Keyclone is *game window* oriented. You define the number of windows (commands), how to run them and what screen region to run them in.
keystrokes are sent to other windows and same for mouse events (if you want them to).
If you have several toons on the same account, they will most likely use the same command and screen position (at startup anyway) and key mappings.

Pros:
- Very easy to get started, and *understand* how it all works.
- create your commands, launch the game instances and BAM, keys are passed from one game instance to the other
- intuitive "do not pass", "overide", key mappings, mouse broadcasting
- cheap, $20 for unlimited usage (per machine)
- Great support from the developer
- Good support from the growing community
- Simple install

Cons:
- very clunky mouse repeater. Once you click, the mouse actually has to move to all other screens to simlutate the click.
- slow screen swapping, depending on machine specs. mine always took 2-3seconds to swap.
- Rob used to be very active on the dual-boxing forums, but has been MIA for some time now (although accessible directly via email/phone)
- latest update is a year old

//-------------------------------------------

ISBoxer is more *game character* oriented. You define your team and characters, and then you give them settings like the screen region or the keymaps. Your toons are in a big character pool, and can be given any of the defined screen regions or keymaps.

Pros:
- easy wizard to get started (but default settings might not match your needs)
- completely customizable to fill your needs, on a character, team or global level
- powerful key mapping with steps, screen messages, macros etc
- in-built FTL support (automatic transparent leader swap when changing main screens for example)
- instant (yes, *instant*, even on my clunky machine) screen swap, when changing which display is main.
- very accurate mouse broadcasting, able to broadcast click to very little objects (talents, bag items, wow addon settings for example)
- real time mouse broadcasting, you see the mouse (or targetting circle :-) on all 5 screens as you move it on the main.
- strong macro making functionality
- everything is virtualized (created on the fly), you don't need to change anything from your solo play
- strong do-not-pass mechanism (white/black list)
- excellent support from Lax, and easy way to contact the developer (Irc channel, d-b forums, innerspace forums)
- Good support from the growing community
- regular updates

Cons:
- it takes a little while to understand how it all works, and how ISBoxers objects (keymaps, regions, characters, broadcast) all interact with each other. Thankfull you can copy and modify things generated from the wizard.
- subscription model. You pay repeatedly. More expensive than keyclone if you multibox more than 3 months.
- more difficult to install than Keyclone. Still quite simple however. I personaly had undocumented errors (cause: old .Net framework, eventually found why on the innerspace forums).
- it took me two nights to get a non-wizarded team to work as i had using keyclones. mainly because i wasn't using the default keymaps from the wizard, and had to understand how to create mine and assign them to the toons.

//-------------------------------------------

TLDR (too long, didn't read):
Keyclone is cheaper and easier, but ISBoxer is so much more powerful that it is worth spending the time working it.
I have keyclone, but have now moved to ISBoxer.


Cheers
-Zub