NotaBene
Originally created in 1983, this writing software was specifically developed for academic writing and combines note-taking, referencing, & writing functionality. It continues to have a small, but dedicated community of users.
Alternatives are typically aimed at fiction or screenwriting, but like Scrivener, they can be adapted for academic writing.
YWriter - First generation and one of the oldest and longest-lived writing software. PC Magazine's Review of yWriter
Free/pay what you want is great, of course, but sometimes the trade-off is bare-bones interface and lack of technical support and help.