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For me definitely Ladybug Tools (mostly Honeybee for energy modelling) and Pollination these days. You can import/export .idf and gbXML files, although the ecosystem is using the HBJSON model schema.

The Rhino license is not free, but it is perpetual compared to Sketchup's subscription system, and it is a pretty robust modelling interface with tons of control over geometry, and built-in visual scripting interface (Grasshopper), that lets you parameterise the models in a pretty flexible manner.

It is way more comprehensive and robust now, than simple shoebox models, a lot happened since the previous reply above.