Off the top of my head:
- Use Transactions.
- Make sure your SQL leverages tables in the correct order.
- Don't add indexes you're not entirely sure you need.
Perhaps not only specific to iPhone but to embedded devices there are some great tips here.
This link pertains to an older version of SQLite but still proves useful.
Lastly this Stack Question also has some good info.
We use SQLite with a .Net Compact Framework Application currently and it's performance is fantastic and we've spent a bit of time optimizing but not nearly as much as we could.
Best of luck.
