Really impressed with Fish: tab completion of command names /with description/, argument completion based on history (a la Ctrl-C in bash)
miniblog.
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One cute feature of markdown I'd not noticed before: there's no syntax for images *without* a description (i.e. alt text).

My favourite pull requests are PRs that are obviously correct after you've read the description.
I'm a fan of simple issue trackers. A description, comments, and maybe a small integration with something.
Given this, perhaps it makes sense to build your own? You get a bespoke solution, and focusing on your main project prevents feature creep.