Not a GUI, but I keep my ~/.ssh/config clean by splitting my configs into folders, and including them in the main ~/.ssh/config.

I have the folder, ~/.ssh/config.d/, and here’s what it looks like:

~/.ssh/config.d
.
├── work
│   ├── dev.config
│   ├── staging.config
│   └── prod.config
└── server
    ├── development.config
    ├── containers.config
    ├── home.config
    ├── pis.config
    └── server.config

Then my ~/.ssh/config looks like this:

Include config.d/work/*
Include config.d/server/*
Include config.d/other/*

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