Pwnboxer is rather limited, compared to IS Boxer or HKN.
The one good point, is that it is really easy to configure, because you don't have nearly as much flexibility in its use.
Anytime I mention that IS Boxer can do something... I usually get the response that the feature could possibly result in a ban, and that Lax is shady... the default, which translates into: Pwnboxer cannot do this, and either I cannot code it in, or don't know someone to code it for me... so will malign IS Boxer.

Pwnboxer doesn't mention that it is a subscription product, but it is.
You have unlimited updates for a year.
After the year is over, the next major update that occurs... will result in your version no longer working.
You cannot continue to use an older version and not upgrade to the latest.

The basic limitations...
You can only box on the one machine; there is no communication between multiple PCs.
The tech support is greatly limited, as there is no IRC client to ask about things, and the user base is much smaller so there aren't as many users to respond to requests on the forums, and Tim is sporadically active... very active for a week or two, and then gone (offering no support) for a while... as opposed to Lax offering phenomenal IS Boxer support all of the time.
Pwnboxer is touted as being the least drain on your system; in reality, its basically as much of a drain as Keyclone or a similar product (in that each window is rendered at the display resolution); IS Boxer renders each window at the full size (you configure) and then scales the slaves down (unless you're using full-screen stacked).

With IS Boxer you have a lot more feature options, to configure you team how you want it.
There are numerous video display options, ranging from picture in picture to stacking everything on top of each other and then using video feeds to display the information you want.
You can create mapped keys, which not only send hotkeys to the game, but can alter how your configuration works.
You can use clickbars, to activate a mapped key by clicking on them instead of using the hotkey.
You can create menus with infinite sub menus and access them from the game your playing.
You can play just about any game, and Lax is quick to add support for a new game that you want to play.
Lax also adds support for various input devices, if you pick up a fancy keyboard or a newer mouse/game-pad etc.