I have had good luck running DOS on ZFMicro modules. I developed application softare on a Windows box using on old versions of Borland C, as well as Microsoft C and GNU to allow you to build commandline programs that run under DOS.
Most PC104/Embedded PCs allows you to redirect the console in the BIOS to a rs232 port.
One project I worked on was a datacollector for a radiation effects experiment. A PC104 FPGA module on a ZFmicro PC104 system acted as a wide parallel port that would collect pulse width signals from PICs being irratiated in a proton beam from an accelerator. The PC104 system was near the beam line and the collected data was send via to rs-232 to a Linux laptop in the control room. I used kermit to transfer files/programs to and from the PC104 system, although I could have used a Compact Flash disk.
Depending on the data rates you could use qbasic to develop applications under DOS.
You can use DOS. Here you can find out heaps C++, C# and VB source code running under DOS and Windows. Some examples show you how to communicate to serial port and. You can make your DOS or Windows controller to be Web-Enabled, link your sensors to your web browsers.