Are there any to-do list apps that focus on organizing research and reference material?

Yes — if you want a “to-do list” app that also helps organize research, notes, and reference material, you’ll probably want a task app with strong note/document support or a knowledge-management app with task features. A few good options:

Best-fit options

• Notion — Great for combining tasks, databases, research notes, reference pages, and project planning in one place.
• Anytype — Local-first, flexible, and good for linking notes, projects, tasks, and reference material.
• Obsidian — Best if you want a powerful note system for research/reference, with task tracking via plugins.
• ClickUp — Strong task management with docs and research/project organization features.
• monday.com / Asana — Better for structured task/project tracking, with attachments and notes, but less “research-first.”
• Todoist + notes system — Good if you want simple tasks, but you’d usually pair it with a separate research tool like Obsidian, Notion, or Zotero.

If your focus is research-heavy

• Zotero — Excellent for collecting, tagging, annotating, and organizing references and PDFs. Not a to-do app, but ideal for research material.
• DEVONthink (Mac/iOS) — Very strong for storing, tagging, and searching research/reference documents.
• Roam Research / Logseq — Good for connected notes and research, with task management built in.

Simple recommendation by use case

• All-in-one planning + research: Notion
• Research notes first, tasks second: Obsidian or Logseq
• Reference/library management: Zotero
• Traditional task manager with docs: ClickUp or Asana

If you want, I can narrow this down based on:

1. Mac / Windows / mobile
2. offline vs cloud
3. academic research vs personal projects
4. simple vs advanced