1. Lectra Notes
Free for real: Everything — unlimited documents, Apple Pencil markup, scanner, lecture recording (new in version 8.0, September 1, 2026), on-device AI study tools, Python notebooks, terminal with Git, SSH, and the Mac app. No tiers, watermarks, ads, or third-party analytics.
Standout: The one on this list with a computing environment: Python notebooks that run on the device, a code editor, and a terminal beside your notes.
Trade-off: Lecture recording is new (version 8.0, September 1, 2026) and untested over a full term; no cross-device annotation sync yet; and it's the newest app here (2026). iPad drawing is Apple Pencil-only.
2. Apple Notes
Free for real: Everything — handwriting with Scribble, audio recording with automatic transcripts (iOS 18.1+), Math Notes, collaboration, iCloud sync.
Standout: Zero setup, deepest OS integration, and free audio transcripts — a feature most rivals charge for.
Trade-off: PDF annotation is basic Markup on attachments, not a paged notebook workflow; no custom paper templates; Apple-only.
3. Microsoft OneNote
Free for real: All core note-taking — ink, scanning, voice capture, and sync across iPad, Windows, Android, Mac, and web (within the free 5GB OneDrive).
Standout: The widest platform coverage of any free option — the pick if you live on Windows or Android too.
Trade-off: PDFs import as flat printouts, which makes annotating lecture slides clunky; Copilot AI needs Microsoft 365.
4. CollaNote
Free for real: Unlimited notebooks, 25+ pens, PDF/PowerPoint/doc markup, real-time collaboration, flashcards, scanner. One-time $13.90 lifetime premium for extras.
Standout: Free real-time collaboration and the closest free match to Goodnotes' notebook-plus-PDF workflow.
Trade-off: Small indie team with reported reliability bugs; some formerly free features (including audio recording) moved behind premium in 2.0; requires iPadOS 18.6+.
5. Flexcil
Free for real: Full pen-based PDF annotation plus its signature gesture: drag text or figures from a PDF into a side study note. One-time $9.99 upgrade rather than a subscription.
Standout: The PDF-to-study-note extraction gesture is unique for working through textbooks; also on Android.
Trade-off: Free caps bite fast — 5 notes of up to 50 pages, 5 folders, watermarked exports — and lasso, text, and templates are paid.
6. Kilonotes
Free for real: Core handwriting, unlimited notebooks, and PDF markup, with a large student-oriented template library behind a cheap membership.
Standout: Handwriting feel that reviewers consistently praise, with strong palm rejection.
Trade-off: Ads in the free tier, cloud sync is a paid add-on, and reviewers report bugs and weak handwriting recognition and audio quality.