I take notes by typing, and use a Mac.
I use a plain text notepad application, and type in mostly-ASCII but don't hesitate to use the full range of Unicode. In particular, I have a customized keyboard layout with gobs of dead keys which lets me type arrows, logic/set symbols, superscripted and subscripted symbols, and Greek letters. (I created the layout using Ukelele, and I'm planning to upload it for others to use.)
(Also note that the default Mac keyboard layout has π, Ω, µ, √, ≈, ∫, ∆, ∂, ∞, ≠, ±, ÷, ≤, ≥, ·, ∑, and ∏ already!)
I also don't hesitate to use LaTeX notation if it's convenient, and invent my own notations; for example, if the lecturer writes $\frac{a+b}{c+d}$, then I write a + b // c + d, where the // stands for a “low-precedence division sign” to make up for the loss of one dimension in the notation.
In the extremely rare occasion where I want to produce a nice LaTeX document and have this note text to start from, I convert it by hand (plus a LaTeX preamble which makes the Greek letters and mathematical symbols work directly without conversion to \alpha etc.) — I've only done that maybe twice. As a general rule, anything that was an assignment to hand in, I wrote in LaTeX directly (including intermediate algebraic steps not included in the final document).
By request, an example. These are my unedited original notes from the fourth lecture of a “Calculus III” class. At the time I was generally familiar with the concepts of this material, but I wanted to make sure to write down the notation (e.g. choice of variable symbols) and terminology (e.g. “symmetric equations”) used in this class.
Lines
Identify by the position vector of a point on the line r_0 = <x0, y0, z0>,
and a vector D = <a,b,c> giving the direction of the line.
Vector parametric equation:
r(t) = r_0 + tD
Parametric equations:
x = x0 + a t
y = y0 + b t
z = z0 + c t
Solve each one for t and set equal to get the symmetric equations:
x - x0 // a
= y - y0 // b
= z - z0 // c
= t
Example 1: Find the equations for the line through these two points
The indentation for grouping is done with tabs, so it's only one keystroke. I probably cut-and-pasted the repeated equation lines rather than retyping them. Note that I have omitted the subscript marker _ in the coordinate subscripts because it is obvious in context.
Here's a later section on partial derivatives. This is where the Greek-incorporating keyboard layout comes in handy — I can write down what the lecturer is showing without having to write out the names of the letters or invent alternate notation (such as [w] to stand for ω, which I did before I made the keyboard layout).
Example 3:
Rewrite ∂u/∂x - ∂u/∂t = 0 [wave eqn with speed set to 1] in terms of the variables
ξ = x - t, (xi)
η = x + t (eta)
∂u/∂x = ∂ξ/∂x ∂u/∂ξ + ∂η/∂x ∂u/∂η = ∂u/∂ξ + ∂u/∂η
∂u/∂t = ∂ξ/∂t ∂u/∂ξ + ∂η/∂t ∂u/∂η = -∂u/∂ξ + ∂u/∂η
∂u/∂x - ∂u/∂t = 0 <=> 2∂u/∂ξ = 0.
Therefore ∂u/∂ξ = 0, u is constant wrt xi, so u is a function only of η.
Therefore our solution is u = F(η) = F(x+t).