It is definetely not C3 so which one is it?

Depends which program you're using. There are three "standards": middle C as C3, middle C as C4, middle C as C5.

Is this the C At the bottom of the violin key?

according to samp but other host may be different

the problem is that the middle C note in real music is C4 (yes, the first line of the Violinkey) but a non-standard in midi. so some take C4 as middle note, some companys strange enough take C3 as middle C so the "real" C3 in this cases is C2 if you want. (the pic from hink's post show it well he put C3 in the roll but in the sheet it's the middle note C4). that leads back to your original question: in your case (if C3 in roll sure is not C3 in your sheet you said) it must be C2 then?!

You also have to remember that some instruments transpose, so the note played is not the one written on a score.

Not only to you get instruments like trumpet transposing to Bb, you have some that are forgotten, such as guitar, which transposes to one octave lower than the note as written.

I do sometimes wonder if guitar is responsible for the lack of standardization and why sometimes middle C is written in different places than where it should actually be.

First I thought I get a satisfying answer from Hink, but now Im really confused.... I dont know why everything is made complicated.

It's really simple... Read on:
Yes, that should be "middle C". In Midi terms it's defined as note #60 (5th octave up from the very bottom.)
Weather that shows up as C3, C4 or C5 depends on your host, where they have put the zero mark. Everything is relative to that.