Successfully running a program requires that three things match:
- CPU instruction set (Eg. x86 in your PC, ARM in your mobile phone, PowerPC in some Apple Macs, Java bytecode for Java Applets, CLI for ".Net"/Mono applications)
- Binary File Format (Eg. PE/COFF ".exe" for Microsoft Windows, .jar for Java Applets, PE32 ".exe", ELF on Unix/Linux)
- Application Programming Interface; (Eg. POSIX on Linux/Unix, Cocoa for Mac OSX, Win32 on Microsoft Windows, Base Class Library for ".Net"/Mono applications).
You can increase the chance of matching all three by having emulators/interpreters (for other CPU instruction sets), by having extra file loaders (for foreign file-formats), and having additional programming libraries providing more APIs.
Note also, that some processors can natively execute more than one instruction set; a PC quite often has x86 and amd64 instruction sets; an ARM processor can execute four: ARM32/Thumb/Java bytecode/ThumbEE. Some operating systems can provide more than one API natively too (Microsoft Windows provides Win32 and POSIX).
For everything else you need extra software. For running Java programs you need the three parts listed above to make it work: a Java Virtual Machine program to run the bytecode; a way of launching Java programs, and a Java Classlibrary for the programs to call. "Java" is a brandname here for several separate technologies originally developed by Sun, but to a user they are often downloaded as one.
The same applies for ".Net", which is a marketing brandname for several different technologies originally developed by Microsoft: The Common Language Run-time/Base Class Library (CLR) are the API; VES is the loader and Common Language Interface (CLI) is the instruction set.
You don't have to download those technologies from Microsoft, from Sun, or from Intel just because they originally invented something. AMD make processors compatible with Intel's standards; both Apache ("Harmony") and Google ("Android Dalvik") both make a Java-like suite; and Mono provides a CLR/CLI/VES suite. The important thing is that everyone uses the same standards, making them compatible. A DVD disc will play on any DVD player that meets the standard, and an HTML webpage will rendering in any Web Browser meeting the HTML standards.
- Mono is a CLR/CLI/VES suite that can run on Mac OSX, MS Windows and Linux.
- Wine is a Win32 API implementation that can run on Mac OSX, MS Windows and Linux.
- You can run Mono on top of Wine, on top of any operating system.
- You can run Wine on top of Qemu, on top of any CPU architecture.
So Mono makes CLR .exe applications run, and Wine makes Win32 .exe applications run. The only thing in common is that the filenames end in ".exe"; the contents are completely different and incompatible, so you need the right one.
Just like a Python interpreter will error when presented with Perl (and vis versa), a CLR interpreter will error when presented with x86+Win32, or JVM+Java bytecode. If you can post a link to the particular program that you're wanting to run, myself or somebody else should be able to tell you the exact instruction set, file format and API it was designed for, and what you need to install on Linux to run it. Hope that helps!
(Sometimes you might even need both. For example, the Openbve train simulator is C# and compiled to PE/COFF+CLI+CLR, but can optionally use C binary plugins compiled for PE/COFF+Win32+x86. In this case, you need a Win32 version of Mono under Wine. If the CPU architecture is also, different that would need emulating; so Mono under Wine under Qemu).