I've interested in using some sort of online note-keeping application. I've seen these two mentioned frequently online, and have briefly taken a look at their websites. As far as I can tell, they are both note-keeping tools. Are there any substantial differences I should know about?
Remember the Milk is a task list application first. The notes are not the focus here and the options are limited when it comes to taking notes.
Evernote is a note taking application and it specializes in that field.
If you need to take notes, use Evernote (or another note taking app but this one is good), if you need to manage tasks/todos and attach notes to those tasks, use Remember the Milk.
The major differences are that Evernote is designed for note-taking, web clippings, and memos while Remember the Milk is focused on tasks with a due date. Evernote can hold many formats of information you find while RTM can send you reminders through email, SMS, or Twitter of set tasks.
Don't hesitate to try both of them out. I use both regularly.