cap infractions:
I haven't played in many cap leagues, but that seems like a pretty severe infraction. The the NHL's route with the NJD and moved their first round pick to the end of the first round regardless of their draft order. If they are already at the end because they are winning (making it much worse), then make it more severe.
Leaving guys on IR:
From my experience, and from what I've read in forums and listened to on podcasts, this is considered to be a legitimate strategy that people should take advantage of. Yahoo prevents you from making waiver wire moves while you have an illegal lineup. If your fantasy software doesn't do that, perhaps instigate that rule.
General Activity:
This is the hardest with any fantasy league. You either have a theme of commitment or you don't. If you don't, then it will be very difficult to enforce any lack of activity unless it is blatently not logging in for weeks/months.
Perhaps set a limit, like someone who doesn't set there lines 3 days in a row, or doesn't 10 times on the year, and it affects a lottery chance for their next years draft order.... but that may require you to introduce a lottery system for the first few picks. One of my leagues does that, drawing the names makes for a fun get together or google hangout event.