How can I make my own microcontroller?

Look here for a good wiki book. I had some coursework I wrote when I was teaching Electronic Eng, but I couldn't find it around. When I was teaching, most of the students were happy to use the schematic capture tools in the Xilinx Foundation package. They've moved onto ISE and WebPACK now. You can download the WebPack for free, which is useful, and it has schematic capture and simulation in it.

If you really want to shine, learn VHDL or Verilog (VHDL seems to be more common where I've worked, but that is only a small smattering of places) and code the design rather than enter it through the GUI.

If you know ANYTHING at all about digital logic design (and some HDL) I rekon you can have a somewhat functional 8-bit microprocessor simulating in VHDL in about 2 days. You're not going to build anything blazingly fast or enormously powerful in that time but it's a good starting point to grow from. If you have to learn about digital design, factor in a couple of days to learn how the tools work and simulate some basic logic circuits before moving onto the uP design.

Start learning the basics of digital systems, and how to build a binary adder. Move on to building an ALU to handle addition, subtraction, and, or, xor, etc and then a sequencer to read opcodes from RAM and supply them to the execution unit.

You can get fancy with instruction set design, but I'd recommend starting out REALLY simple until you have your head around whats going on, then throw it out and start again with something more complex.

Once you have the design simulating nicely you can gauge its complexity and purchase a device to suit. You should look at a development system for the device family you've chosen. Pick a device bigger than what you need for development because it's nice to be able to add extra instrumentation to debug it when it's running, and you almost certainly won't have optimized your design in the early stages of getting it on the device.

EDIT: Colin Mackenzie has a good tutorial about uC design and some FPGA boards as well as a bit of other stuff.

You may want to have a look around OpenCores.org, a "forge" site for open source IP core development. Also, consider getting yourself a development board like one of these to play around with.

Much of the tools ecosystem revolves around VHDL, although Avalda is working on tools to compile F# for FPGAs.