Any of the encryption algorithms should work, provided they are implemented correctly, and the data is passed between the systems without modification. So start looking at what standard algorithms are implemented on the linux system, and see if they have equivalents implemented already for Windows / .NET
Probably the place to start is with the MCrypt documentation:
mcrypt(3): encryption/decryption library - Linux man page[
^] - certainly, it includes Triple DES which is definately available to all .NET languages.