I put repair tools at the bottom of my pannier because I almost never use them. But then when something goes wrong, I have to empty my pannier to reach them.
If I'm not carrying a saddle bag, rain gear would be in a pannier too.
That's all I can think of.
Tools, I usually have a tiny little multi-tool in my pocket on a tour. Other tools and spares being quite dense (small and heavy) are in the bottom of a rear pannier. Last time I needed to dig out the tool bag while on the road was eight years ago when I needed to get my cassette lockring and other tools out. Major hassle, but at least it was not raining.