The Star Trek: TOS episode "This Side of Paradise" probably fits, the plant spores work to create a "perfect environment" of health & happiness, the plant spores actually have a parasitic need for human hosts.
I don't remember which episode of the Animatrix, but there was an athlete, who momentarily exited the Matrix through sheer force of will during an intense race. The ending scenes showed a broken man in a wheelchair, carefully watched over by Matrix Agents. I don't know if this would qualify as a sub-point under The Matrix, or should get a separate entry.
Perfect Blue can be interpreted this way, especially if you allow for one's brain to be said machine.
In Virtuosity, the protagonist uses one on the villain to acquire information about hostages. Despite his implied brilliance, the villain swallows it whole.
The game Hell: a Cyberpunk Thriller has a very unhappy one: political prisoners are given realistic torture impressions by a Lotus Eater Machine, and they actually believe they are in hell.
Edited by SolariusScorch
In Dyson Sphere Program, the main character (the Engineer) is not in Cyberspace, but the rest of humanity is. As (I assume) entering cyberspace was consensual - does this count?
"What I don‘t like about measure theory is that you have to say 'almost everywhere' almost everywhere." - Attributed to Kurt Friedrichs