Total Phase software seems to come closest to the real thing so far. But I don't understand why they must have two boards (Aardvark and Beagle) to do almost identical things. Baring that, the software is key and it looks to be the best out of the bunch. Enterprise-level pricing, but still ok.
Yes, BusPirate is opensource, but so is any dev board. There is nothing really special about it. The only positive point is that it can be used independently (sort of) without any software or host PC. There's not something even close to scripting unless you consider making scripts in python to: press P, check if this thing outputs some menu, press another key, read back screen, ... Good luck trying to read a 1Mb SPI flash in a decent amount of time. I still use it from time to time though.
I've seen scanalogic but I cannot figure out if they can output the decoded protocols. I only see FM, PWM, USART in the output window. And decoding is only half the job, I don't see any encoding features. It's really cheap though, less than what I paid for the bus pirate.
I think I'll just stick to my current solution for now and maybe develop a small open-source Java tool/firmware combination. When I say firmware I really mean sketch. The firmware side should translate I2C, SPI and other protocol logic to [virtual serial?] USB I/O. That's because just shifting the bare pin changes via USB is really slow. Everything else can be done on the PC/host side in some Python script. Java can take a python parser as a library and can provide nice portable GUIs.
Side rant: I really hate when Linux-lovers get their hand on software and in order to use it on Windows you have to go through ten thousand hoops: download GTK, cygwin, python. That is if you are lucky and it's actually compiled. It's a virtual fence that keeps honest and willing people out. I'm looking at you: gimp, sigrok, octave, ... I keep some VMs ready for that but <10% of the programmers I know actually want to go through that trouble.