Where did all the output writers go?
I miss my FLAC, lame and ogg. How can I "fix" it?

Didn't find any info, maybe i'm just a lousy searcher...

In case you are talking about the recent Betas, you will have to add the new presets you want using the add button under output presets.

In my opininon quite a nice feature, scince it keeps the preset menu slightly less cluttered. Had me baffled for about a second as well though.

But now I can't set compression/quality in foobar anymore when using flac/lamer etc.

Did you actually install any of the output writers?

They are included in the special installer or available here

Otherwise the options are still available in their respective config menus.