What is the best visa option for spending 3 months in Thailand as an Australian married to a Thai citizen?

Tourist visa IMHO less hassle.

As the question is the best visa:

The Non Immigrant O visa based on marriage with a Thai National, reason is that you get 90 days on entry and possible to extend with another 60 days based on visiting wife.

The Tourist visa gives you only 60 days, can be extended once with 30 days (cost 1900 Thb) and after those 30 days you can apply for the 60 days to visit wife but that cost again 1900 thb and an extra half day sitting in an Immigration Office.

Save time and money to apply direct for the correct visa.

90 days Non-O following thai wife. That way you dont have to get the extension.

Either get a Tourist Visa (60d) and extend it (30d) or get a non-O visa for 90 days.

Get a 90 day Non-O visa. Reason, visiting or staying with applicants family resided in Thailand (more than 60 days), easy to do. You can write a letter of invitation with the approval of your inlaws, include a copy of their ID card in the letter.

A Thai tourist visa will give you 60 days on arrival plus 30 Days extension of stay = 90 day stay in Thailand.

Where aren't in Australia ?