I've used Linux Multimedia Studio, It's free and runs on linux, windows and mac. It has lots of preset instruments, and allows you to tweak them to sound different. You just have to read the help file a couple of times to find where the presets are, and how to place notes. It handles midi input from electric keyboards.
It also has sine and square waves, which I think is used for games on the NES / GB.
Edit:
lol, didn't notice you'd already tried it!
You could try soundclub, it's also free. I used this before LMMS, and it's really simple to use. It says it's for windows 95/NT, but I've used it on XP too. You can use the mouse to plot down notes, along with midi input from a electronic keyboard too.
http://www.bluemoon.ee/history/scwin/It's pretty old, so it was hard to find in google again, but if I wasn't using LMMS, I'd still be using this.