Actually I've been put right by the help guys there. Do you use the Master Doc feature or just one mammoth file (mine is currently 300K)?
I tried using the master doc but found it awkward, so just the one mammoth file - the current WIP has multiple parts at around the 250k mark, except for one that got a bit bloated at 350k. I also make extensive use of the notes feature, especially during editing, although big files with a lot of notes run like a three-legged dog trapped in treacle. (Or, more literally, type a key, count a few seconds, see the screen update...)
I use Libre Office, a more up to date branch from Open Office. The biggest advantage is that it supports conversion to docx, not just doc file format.
I am currently making the transition to Libre Office. Up until quite recently it had along-standing bug in the spellchecker which meant that any word with a note boundary inside it would flag as misspelled regardless of the whether it really was. The bug has a second part that if you accept a correction on a word containing a note boundary, the note is deleted. Now that part 1 is fixed I am making the move. Part 2 is actually a serious, data-loss issue, but it turns out that the same bug exists in Open Office, so that's not a reason to hold back. On the massively positive side, notes do not drag the speed down in Libre Office.
(There is another bug where those note boundaries confuse the search function.)
I keep character notes and plot ideas in a separate file and recently I have started using Zim wiki to keep track of things, but that's mostly because the current WIP is in five books and it's a pain to keep searching five separate files for stuff now that I'm in the post-pantsing phase of making things consistent.