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Though an emulator is quite useful for debugging code that has no side effects, most real-world applications include some circuitry besides the Arduino. If a microcontroller on an Arduino had a JTAG interface, it would be pretty straight-forward, but what if it's e.g. an Arduino Uno?

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Could you elaborate on what you are trying to accomplish? Its not clear from the question that what exactly do you want to debug. –  AsheeshR Feb 27 at 12:24
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@AsheeshR The only thing that is possible to debug on Arduino is source code. There's a set of tools called "debuggers", which employ breakpoints, step-by-step evaluation etc. I don't understand your question. –  polkovnikov.ph Feb 27 at 15:12
    
@jippie You're wrong about that. DebugWire yes, but JTAG No. The ATMega168/368 has no JTAG support whatsoever. If you do a quick search of the datasheet you will not find any reference to JTAG –  Madivad Feb 27 at 15:15
    
@Madivad Is it possible to make another Arduino into USB to DebugWire connector? –  polkovnikov.ph Feb 27 at 15:17
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It seems there is possibility for interactive debugging with this tool: visualmicro.com/post/2012/05/05/Debug-Arduino-Overview.aspx it is not free but it is quite cheap. I haven't used it myself so I don't want to provide an answer for it. –  jfpoilpret Feb 27 at 22:47
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The Arduino Uno uses the Atmel Atmega328p microcontroller, which only has one debug option, DebugWire. There are a few tools that can work with it, but the least expensive and most commonly available is the AVR Dragon.

You can use AVR Studio 6 for this. You can use the .elf file file produced during the Arduino build process directly, but setting up the debugger is a little easier if you port the Arduino program to the AVR Studio. It's not difficult, but there are a lot of little pieces to deal with. There are guides online to help you through this.

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Is there an AVR Dragon clone with open-source firmware? –  polkovnikov.ph Feb 28 at 13:28
    
Any links to those online guides? –  polkovnikov.ph Feb 28 at 13:30
    
There are MKII clones which will do debugwire with this chip, but I'm not aware of their open source hardware or software status, and am having trouble finding a good example easily. Here's one guide for using AVR Studio 6 with arduino projects: engblaze.com/… –  Adam Davis Feb 28 at 15:48
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