I think I read somewhere that the EEA permit was free but if you wanted your non EEA spouse to work, you filled out another form which costs £59.
Not quite. The non-EEA spouse automatically has the right to work in the UK anyway.
The EEA family permit is free and allows you to work (you have the right to work anyway, but the permit is just confirmation of that right). However, it is only valid for entry to the UK and is only valid for 6 months, so you have to apply for another visa anyway, whether you are planning to work or not.
The 5-year EEA Residence card is what you apply for after you arrive in the UK on the EEA Family Permit, before the 6 months are up. You can work before you apply for it and during the processing time (which can be 6 months). It used to be free of charge, but they introduced a fee of £55 on 1st July 2013.
After 5 years on the EEA Residence Card you can apply for confirmation of permanent residence. This also used to be free, but they introduced a fee of £55 on 1st July 2013.
So, what used to be a completely free process all the way up to
citizenship permanent residence now costs £110.