"Building a second brain" has become a cottage industry. Notion, Obsidian, Roam, Logseq, Apple Notes, and now AI-powered newcomers. But which tool actually helps you think better? Here's the honest breakdown.

Quick Navigation

Notion — The all-in-one workspace
Obsidian — The graph-based PKM
Roam Research — The original backlinker
Apple Notes — The default choice
Thoughtmarks — The capture-first approach
The Verdict — Which to choose?

Notion

Notion wants to be everything: notes, wikis, databases, project management, docs. And it's remarkably good at being everything—which is both its strength and weakness.

✓ Strengths

• Extremely flexible
• Great for structured data
• Beautiful templates
• Team collaboration
• Database views

✗ Weaknesses

• Slow on mobile
• Steep learning curve
• Online-only (mostly)
• Can feel overwhelming
• Easy to over-engineer

Best for: People who want one tool for everything and don't mind spending time setting it up. Teams. Documentation. Project management with notes attached.

Not for: Quick capture. Mobile-first workflows. People who want simple.

Obsidian

Obsidian is the darling of the PKM (Personal Knowledge Management) community. Local-first, markdown-based, endlessly customizable with plugins. The graph view makes you feel like a genius.

✓ Strengths

• Local-first (own your data)
• Pure markdown files
• Powerful backlinks
• 1000+ plugins
• Graph visualization
• Free (sync is paid)

✗ Weaknesses

• Steep learning curve
• Plugin rabbit hole
• Mobile app is okay, not great
• No native voice capture
• Manual linking/organizing
• Can become a hobby itself

Best for: Tinkerers. People who enjoy building systems. Writers who think in connections. Privacy-conscious users.

Not for: People who want capture without configuration. Those who get lost in productivity porn.

Roam Research

Roam pioneered bidirectional linking in mainstream note-taking. The daily notes format and block references were revolutionary. It built a cult following—and a $200/year price tag.

✓ Strengths

• Block-level references
• Powerful queries
• Daily notes workflow
• Passionate community

✗ Weaknesses

• Expensive ($200/year)
• Steep learning curve
• Cloud-only
• Slow development recently
• No mobile app (web only)

Best for: Researchers. People who think in connections. Heavy outliners. True believers in networked thought.

Not for: Budget-conscious users. Mobile-first workflows. Quick capture needs.

Apple Notes

The default that ships on every Apple device. Simple, fast, syncs automatically. Don't underestimate it—Apple Notes is genuinely useful.

✓ Strengths

• Free and pre-installed
• Fast and reliable
• Seamless Apple sync
• Supports rich media
• Good search
• No setup required

✗ Weaknesses

• Basic organization (folders only)
• No backlinks/connections
• Limited formatting
• Apple ecosystem only
• Voice memos are separate

Best for: Simple needs. Shopping lists to project notes. People who don't want to think about their notes app.

Not for: Knowledge management. Finding connections. Advanced organization.

Thoughtmarks

Full disclosure: we built this. But here's the honest take. Thoughtmarks is different— it's capture-first, not organization-first. Voice input, AI organization, semantic search. The anti-Obsidian.

✓ Strengths

• Voice-first capture
• AI auto-organization
• Semantic (meaning-based) search
• Apple Watch app
• Siri integration
• Zero setup required

✗ Weaknesses

• iOS only (for now)
• Less customizable
• No graph view
• New (smaller community)
• Paid ($60/year)

Best for: People who hate organizing but love capturing. Voice-first workflows. Apple Watch users. ADHD brains.

Not for: Android users. People who want full control over organization. Graph visualization enthusiasts.

The Verdict: How to Choose

There's no "best" second brain app—only the best one for how you actually work. Ask yourself:

"I want to build elaborate systems"

→ Obsidian or Notion

"I want quick capture without thinking"

→ Thoughtmarks or Apple Notes

"I want team collaboration"

→ Notion

"I want AI to handle organization"

→ Thoughtmarks

"I want free and simple"

→ Apple Notes

Try Thoughtmarks Free

If capture-first sounds right for you, give Thoughtmarks a try. 14-day free trial, voice capture, AI organization, semantic search.

$5/week, $15/month, or $60/year after trial.