I think the closest you'll get is the the eclipse "NotePad" plugin. It doesn't create footnotes directly, but rather just takes plaintext notes and puts them in the metadata. You'll find it at: http://eclipsenotepad.sourceforge.net/
Better, though, is to use eclipse's built-in indexing, and leave yourself
/* @TODO 1) take note of this notey note */
comments near important lines.
"But sleepynate", you may say, "that's madness! I don't have anything TODO there!"
While this is true, eclipse automatically indexes certain comment tags, like @TODO
and @FIXME
, and puts them in your "Tasks" window. (Window > Show View > Tasks if yours is currently hidden. You can then double-click any one of them to jump to that line. You can also arbitrarily add tasks from the Edit menu with whatever label you want, in any resource and location within your project.