I'd really like to export to .AI so I can import into Toon Boom Studio, but my Inkscape doesn't have the option. I checked the log file but there is nothing mentioning anything missing for .AI files.

Do I need Illustrator installed for this? I'm running Windows 7 if that helps.

Try exporting to PDF (currently save a copy -> ... PDF) then changing the file extension to .ai
Adobe Illustrator's native format is a PDF with some extra editing meta-data, most other programs (including Inkscape) use the fact that it is basically a PDF to do the import from .ai files.

Your mileage may vary...

I'll give that a try, thanks!