You can just buy the microcontroller and do it yourself from there. Here is a nice example someone did of a simple LED flasher [1] with just 6 parts:

1. An ATmega ATTiny85 microcontroller

2. A socket for that processor

3. A coin cell battery

4. A holder for the battery

5. A resistor

6. An LED

and some wire and solder.

What going with an actual Arduino or Arduino compatible gets you, from a hardware point of view, is a bunch of ready made attachments. For instance, suppose you have some sensor that needs an odd voltage and has weird timing requirements. It will be a lot more convenient to get a shield that has that sensor, and a voltage converter, and something that deals with the weird timing and presents a simple I2C interface to your code than to have to do all that yourself.

There are some EdX courses that you might find useful.

From UTAustinX, "Embedded Systems--Shape the World" [2]. This is a lab-based course where you do 13 or so labs using a TI Tiva Series C Launchpad. That's an 80 MHz ARM Cortex M4 board. Cost for the hardware for the course is $35-$55, depending on if you want to do a couple of the optional labs.

From UCBerkeleyX, "Electronic Interfaces: Bridging the Physical and Digital Worlds" [3]. Another lab course

From MITx, "Circuits and Electronics" [4]. The online version of MITs 6.002 introductory electronics course.

[1] http://forum.arduino.cc/index.php?topic=200590.0

[2] https://www.edx.org/course/embedded-systems-shape-world-utau...

[3] https://www.edx.org/course/electronic-interfaces-bridging-ph...

[4] https://www.edx.org/course/circuits-electronics-mitx-6-002x-...

Have you seen mbed? http://developer.mbed.org/platforms/ Not used it for a couple of years myself, but it seems to have expanded in scope a lot recently.

Was very quick to get started hacking (can program over usb from the free cloud-based IDE), and some of the boards are under $15.

Another vote for mbed, their Cookbook can get the tedious stuff out of the way for most projects: https://developer.mbed.org/cookbook/Homepage

We're using NuttX, a POSIX-like RTOS (https://en.wikipedia.org/wiki/NuttX) as the base for Thingsee One (http://www.thingsee.com).

Wikipedia has a list of supported MCU-families.

An arduino or arduino clone still seems like the best bet to me, in my amateur opinion. Nowadays you can get an UNO clone for $4, and that gets you pin compatibility with Arduino shields, plus loads of guides and help interfacing with other components. I still have a Freaduino Micro (besides my original Duemilanove) and it works fine.

And the Arduino can be programmed in C; in fact, the "Arduino language" is just C (or C++ nowadays?) with some preprocessing and a bunch of helper libraries.

These are my personal favourites: https://www.pjrc.com/teensy/

I've also extensively used PIC24's and they're great (fast, cheap, feature-rich 16bit microcontrollers) but I don't know of any existing boards using them (I made my own) and there isn't nearly as much documentation/sample code/libraries as there is for Arduino and clones.