A few more ideas:

- Growl/Notification center notices for new stories (optionally configurable by a certain points threshold).

- Subscribe to certain topics (keyword based searches). Only get notified when certain topics have stories.

- Ignore stories by user.

- Search (both locally and offer to use hnsearch.com)

- List new submissions (separate tab?).

- Comments/open hotkeys (previously mentioned here, I see).

- Minimize to Mac OS menu with an icon indicating new stories (follows your notification threshold and/or topic subscriptions).

- Tab to monitor your own submissions.