Ways to treat disorganized thinking, other than pharmacotherapy Disorganized thinking is a cognitive deficit symptomatic of thought disorders such as schizophrenia. This affects your ability to process and connect thoughts and ideas, rendering them disorganized, and fragmented. In extreme cases, disorganized speech results.

Are there any activities that have a therapeutic effect and remedy this somewhat? For example, puzzles, computer programming, writing a novel etc. Or employing certain new habits. For example, composing mind maps, writing lists of tasks on your arm etc. Finally, there's cognitive remedial therapy (CRT), and other forms etc.
Metacognitive therapy has been proposed to improve disorganized thinking. Metacognition can be thought of as our ability to "think about thinking." Essentially, it's a person's ability to organize their thoughts into a coherent narrative, reflect on their thoughts and experiences, take the perspective of others, and make sense of the world. Individuals with schizophrenia and other forms of psychosis may experience disorganized thoughts, which can hamper their metacognitive ability. They may even have difficulty recognizing that other people would have thoughts or emotions about other peoples' lives or behavior. 

Metacognitive therapy can take different forms, but in many cases it involves helping people organize their thoughts by eliciting narratives about their lives. For example, a therapist may ask a client to tell them about a recent trip to the store, or an event that was meaningful to them. If the client responds in a disorganized manner, the therapist can drill down to details, focusing on helping the client organize the story. 

For example, imagine a client is telling a story about attending a basketball game, but has left large chunks of the story out, or has skipped around chronologically. This type of exchange might occur:

Therapist: "It sounds like you had fun, but I'm confused. When did you arrive at the game?"

Client: "Oh, about 7."

Therapist: "And did you go to the game with your friends, or meet them there?"

Client: "Sam and I met Bob there."

Therapist: "Oh, so you and Sam drove over to the game at 7pm, and met Bob."

Client: "No, Sam and I came separately, but we met up first at the game. Then later we saw Bob."

In this exchange the therapist keeps pulling for additional details, helping the client recall and organize the experience by re-telling it. The therapist also "inserts her mind" into the discussion by admitting "I'm confused." This tells the client that a) their story was not clear and b) the therapist is having thoughts and reactions to hearing the story. Over many sessions, metacognitive therapy may help clients organize their thoughts, and become more aware of other people's internal experiences. 

This was a very brief explanation, and I've listed a series of papers and books about this type of intervention that can provide additional information. There may be other therapies that address disorganized thinking, but this is one I am most familiar with. I will expand this answer in the future, if time permits. 

References


Brune, M., Dimaggio, G., &amp; H Lysaker, P. (2011). Metacognition and
social functioning in schizophrenia: evidence, mechanisms of
influence and treatment implications. Current Psychiatry Reviews,
7(3), 239-247.
Dimaggio, G., &amp; Lysaker, P. H. (Eds.). (2010). Metacognition and
severe adult mental disorders: From research to treatment. Routledge.
Hasson-Ohayon, I., Kravetz, S., Levy, I., &amp; Roe, D. (2008).
Metacognitive and interpersonal interventions for persons with severe
mental illness: theory and practice. The Israel journal of psychiatry
and related sciences, 46(2), 141-148.
Lysaker, P. H., Gumley, A., &amp; Dimaggio, G. (2011). Metacognitive
disturbances in persons with severe mental illness: Theory,
correlates with psychopathology and models of psychotherapy.
Psychology and Psychotherapy: Theory, Research and Practice, 84(1),
1-8.
Salvatore, G., Conti, L., Fiore, D., Carcione, A., Dimaggio, G., &amp;
Semerari, A. (2006). Disorganized narratives: Problems in treatment
and therapist intervention hierarchy. Journal of Constructivist
Psychology, 19(2), 191-207.
Salvatore, G., Lysaker, P. H., Gumley, A., Popolo, R., Mari, J., &amp;
Dimaggio, G. (2012). Out of illness experience:
metacognition-oriented therapy for promoting self-awareness in
individuals with psychosis. American journal of psychotherapy, 66(1),
85-106.