I think the basic problem is that MIDI defines notes by note number 0 to 127, but humans most easily think in terms of 12 notes per octave, the names of which keep repeating as we go through the octaves. Any music reader knows what "the C an octave above middle C" means, but to think of notes in terms of 128 numerical values is like thinking about websites as http://123.456.789.012:80 rather than www.some-domain-or-another.com, or handling large numbers in binary rather than the much easier to cope with decimal or hexadecimal.

So manufacturers started referring to notes as B1, F6 etc. and the conventional use of "piano roll" MIDI editors relating to a keyboard graphic.

Edited to add that the domains used are entirely fictional and there's no link code there despite to forum software pretending otherwise.

I'm guessing somewhere it came down to:
 
C0 C1 C2 C3 C4 C5 C6 C7 C8 C9 C10
vs
C-1 C0 C1 C2 C3 C4 C5 C6 C7 C8 C9

Starting my midi life with an Atari all editing was done using the numbers C1 etc. There was no Piano view,,, just the event list. You got good at working with drum parts D2-C2 and F#3  snare -Kick-hat. 
The values always worked until my buddy bought a Yamaha FB01. It was off by an octive. Seemed Roland and Korg stuck to normal values and Yamaha had to be different just to be different. 
I still have those old midi files and when I load them have to transpose the bass track. 
It's addictive drums that's messing with my old brain...F#3 is now a cowbell or something...

I think Propellerhead Reason uses C3 as middle C and I had Reason before Sonar (I started with Home Studio 4 or whatever it was called).
That would explain why I think Sonar is off.

Grum.

The tip above is fantastic, thanks.  I use a lot of virtual instruments with keyswitches (most importantly, Vienna Symphonic, RealGuitar, and Hollywood Strings) and this has always been a matter of trial and error.

rabeach
The Scientific Pitch Notation is the American Standard Pitch Notation. The USA has not even adopted the International System of Units (SI) so I wonder by what authority is the American Standard Pitch Notation being referred to as the Scientific Pitch Notation.:-)
 
Scientific Pitch Notation is not a part of the midi specification. Midi specifies frequency by addressing five octaves below and above middle C and assigning midi note 60 to middle C. Nowhere is C4 specified as the pitch notation for midi note 60 or is the Scientific Pitch Notation adopted in the standard.

Sorry if my point was ambiguous. The MIDI spec is, as you note, mute about the use of octave notation. It does define a middle C note number, from which one can logically derive the octave location of the other MIDI note numbers. The confusion suffered by the OP and others comes from the fact that the notation of the correct octave by various designers of MIDI devices is not standardized to a common notation. To find such a standard, they, and the musicians of the world, would need to look outside of the MIDI spec to a widely accepted standard. There are historically a bunch of ways that octaves have been referenced including by name, location on various instruments, use of alphabetical abbreviations etc. American Standard Pitch Notation was put forth by the Acoustical Society of America in the 1930's as a simple standard using a note name followed by a number to indicate the octave, which can be easily recognized and converted to a frequency by someone who does not read music (scientists and the like). Whether this system is more scientific than say the Helmholtz system is arguable, but it is actually more widely recognized by that name than by the American Standard appellation, and is the only way you are likely to find octave notation in scientific articles. In any event, using the style of the scientific notation system but moving the middle C to C3 or  C5 can only cause unnecessary confusion. 
 
There is also some confusion introduced by the use of the term scientific pitch to define an even tempered scale based on C4=256 which is favored in physics textbooks and articles because it allows all the C's to be whole numbers in the binary system. The standard accepted by most musicians is the International Standards Organization Acoustics -- Standard tuning frequency (Standard musical pitch) iso16:1975 which sets A in the treble clef to 440 Hz +or - 0.5 Hz, putting C4 at a mathmatically less attractive 261.62 Hz.
 
Système International d’Unités (SI, International System of Units) does not include a musical pitch designation at all but uses a derived unit of frequency, the Hertz 
 
 

slartabartfast
 
Système International d’Unités (SI, International System of Units) does not include a musical pitch designation at all but uses a derived unit of frequency, the Hertz 
 
 

sorry, if my humor was not obvious...

Thanks, everyone.  Great info and an ideal solution.