WeeChat with the wee-slack plugin is pretty good (https://github.com/wee-slack/wee-slack). That doesn't help folks that don't use WeeChat though.

I have been investigating Riot/Matrix lately. One of the things that really bothers me about the Slack desktop client is its lack of multiple windows. Participating in more than one conversation at a time is a flurry of clicks/keystrokes to keep up. Unfortunately the Riot client doesn't appear to have multiple windows either and the status of the Slack gateway is somewhat unclear.