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I use u-boot for a boot loader. As for init and libc, I just use systemd and glibc.

Boot time is not a bottleneck for my application (however long it takes, the client will take longer…), and I’m sure there’s some more optimal libc to use, but I’m not sure the juice is worth the squeeze.

I’m also interested in what others are doing.

You aren't likely to need to change a lot of these: the whole point is basically making it so that all that can run as normal but won't really get in the way of your high-priority process. It's just that your high-priority process needs to be careful not to block on anything that might take too long due to some other stuff running. In which case you may need to avoid certain C standard library calls, but not replace it entirely.

I guess U-boot, uclibc, and busybox is quite common starting point.

Of course, this varies immensely between different use cases, as ”embedded Linux” spans such a huge swath of different kinds of systems from very cheap and simple to complex and powerful.