I'll try to confine my response to formats that OpenToonz supports but please understand that formats I mention can be a bridge to other formats with transparency that OpenToonz doesn't support.
PNG is likely the most prevalent and will be the option used for most users.
It it isn't always the best format (no format is) but I use it all the time and it is currently my default format type in OpenToonz because... my target for the final image out of OpenToonz is usually the internet.
I would say the GIF animation format is my primary format (and it often is) but transparency is currently not supported.
PNG is an optimal format if your images will be displayed at any time in a web browser.
More robust formats that support transparency include TIF, TGA (targa) and EXR. (The EXR format is currently not directly supported in OpenToonz).
TGA is a rock solid format but not one that will display in a browser.
I think PNG should work for your purposes.
If you discover it doesn't consider a format such as TGA.