What I usually do for plot is I start with the major points (beginning and climax), then fill in major story beats between them. After that, if I get an idea for a scene that I want to include, I find which beats I want it to go between and jot it in. This is all in point form, preferably in a word document, but a notebook works too, and sometimes the feel of writing with a pen when planning is amazing.
I take my time with this outline, so that when I'm writing it's more like walking across stepping stones. It also helps when life gets in the way and I can't write for a month. I won't forget my ideas because everything's written down where I can refer back to it.
@HollowEve Last I checked, Smart Ideas was still around, but it's a one month free trial and then you have to pay for it. If you already have the Microsoft suite that includes word and powerpoint, then I'd recommend looking at visio, it's pretty similar.
EDIT: Looks like I made a mistake. Visio may not be part of that package after all. It's still a great program for the task, but not a free option.