Well, for one, I'm a Pentadactyl user just like slowpoke, but also of DownThemAll!, NoScript (from everything I've read, NotScripts is a poor clone - no offense to the developer, as I said, they're limitations of the browser API) and some others.

In the past, I've also used my own extension, that allowed me (and the few hundred other users) to select a piece of text and launch a terminal using it as a command. Absolutely impossible to do in Chrome.

Finally, Tiddlywiki - only usable in Chrome if you install and run a Java program (applet?). Since I don't have Java in my work laptop, no dice.

As for the iPhone, simply installing non-approved apps; old console emulators, for example.

Not the parent, but for Chrome, probably the horribly limited extension API. I could not even begin to imagine how I would use a browser without Pentadactyl. Or Tree Style Tabs. Both of which are flat out impossible in Chrome. As are tons of other extensions.