I use quadrille ruled paper with the 1/4" squares. I try to lay it out to scale and don't worry about drawing the details. Then I add notes about where rabbits, dados, and the like, go with appropriate dimensions scribbled somewhere on the paper. Sometimes I also have a 2nd page with more notes. Sometimes I'll draw out a detail so I don't forget my thought process.
I also like not being tied to the computer screen. I can sit in the easy chair in the evening with a beer next to me, sort of listening to the TV, and sketch away.
For me, the big thing is then letting the drawing age and look at it a couple of more times during the course of a week or two. Usually I'll revise something because I overlooked something or have a better idea.
I have done everything from simple bread boxes to full blown complete wall bookcases to even a 1000 sq ft addition (that was done on bigger flip chart paper) this way with great success. Usually when I make whatever it is I take some real measurements as I go along to determine things like exactly how long are these 4 pieces of horizontal face frame. Many parts I can just layout, measure, and cut as I go when I get to the final trim.
Also when it comes to some standalone piece I can 'change it on the fly' a little if I happen screw up some initial cut.
Someplace I'd like to use/find software to help me though is to figure out a cut list for cutting up plywood. I have 2 built in bookcases to make and each is going to take probably 10 sheets of mahogany plywood. I'd sure like to be able to plug in A number of this size, B of this size, etc and have the software tell me how many sheets I really need and how to cut them (with the grain all running the same way). Particularly at $80-$100 a sheet and with probably 15 different sizes involved.
