There is some work that has been used in classroom environments. This work has relied on log files, human observation, web-cams, other sensors, or some combination of these inputs to detect student affect. 

Pardos, Z. A., Baker, R. S. J. D., San Pedro, M. O. C. Z., Gowda, S. M., & Gowda, S. M. (2013). Affective states and state tests: investigating how affect throughout the school year predicts end of year learning outcomes (p. 117). ACM Press. http://doi.org/10.1145/2460296.2460320

Bosch, N., D’Mello, S., Baker, R., Ocumpaugh, J., Shute, V., Ventura, M., … Zhao, W. (2015). Automatic Detection of Learning-Centered Affective States in the Wild. In IUI 2015 (pp. 379–388). Atlanta, Georgia, USA: ACM Press. http://doi.org/10.1145/2678025.2701397

A self-reporting method called experience sampling can also be used and combined with other data collection methods to reduce participant burden or build affect detectors so that you can reduce or remove your dependence on self-reporting:

Clayton Epp, Michael Lippold, and Regan L. Mandryk. 2011. Identifying emotional states using keystroke dynamics. In Proceedings of the SIGCHI Conference on Human Factors in Computing Systems (CHI '11). ACM, New York, NY, USA, 715-724. DOI=http://dx.doi.org/10.1145/1978942.1979046

Carrie Demmans Epp. 2016. English language learner experiences of formal and informal learning environments. In Proceedings of the Sixth International Conference on Learning Analytics & Knowledge (LAK '16). ACM, New York, NY, USA, 231-235. DOI=http://dx.doi.org/10.1145/2883851.2883896

When I used experience sampling, 11 of my 12 participants submitted enough reports for me to use the data. The bigger challenge with this approach is getting people to start the study. If you go the self-reporting route then I would recommend combining it with another sensor or data collection method. There has been discussion about using smartwatches or fitbits to support affect detection but I haven't seen any papers on that yet.

Thanks a lot for the valuable articles and for sharing your experiences!

I have previously found some studies which proposed measurement in the field using these methods, for example:

Schellhammer, Stefan; Haines, Russell; Klein, Stefan (2013). Investigating Technostress in situ: Understanding the Day and the Life of a Knowledge Worker Using Heart Rate Variability. In Proceedings of HICSS 2013, IEEE, 430-439. DOI: 10.1109/HICSS.2013.365

Also, I found some studies which applied experience sampling, for example in combination with a consumer-grade level chest strap for HR measurement:

Atz, Ulrich (2013). Evaluating experience sampling of stress in a single-subject research design. Personal and Ubiquitous Computing, 17(4), 639-652. DOI: 10.1007/s00779-012-0512-7

Though, so far I had found no studies which collected real-time data of actual human-computer interactions (such as file activities or switching between programs), without simulating the environment, mostly due to data privacy concerns of involved organizations.

The Epp, Lippold, and Mandryk study gave participants an option to review the keystroke data that they would be sending and decide to not send sensitive data. They also didn't track the first ~10 minutes of a user's keystrokes (after they logged in) because it was likely to contain passwords.

My participants were encouraged to send me pictures but I asked that they not send pictures from personal spaces and gave the washroom and their bedrooms as an example. I did this for two reasons. I didn't want that data and I wanted them to know that I wasn't interested in deeply personal information so that they felt comfortable.

Using these types of approaches often means developing a relationship with your participants. They need to know that they can trust you. In an organizational setting, this will mean that someone who is influential will need to trust you and probably introduce you to your potential participants. The person who performs the introduction probably shouldn't be included as a participant because of the potential bias that your relationship introduces.

We studied a scenario at Humboldt innovation that facilitates solutions in the context of an assessment center and relies on a game-based environment (see link). We adapted a system initially developed at Humboldt-Universität zu Berlin realized as a Java software. Please take a look and contact me if you need more information.

http://socioware.de/SlimAC/