Note: These suggestions aren't Regex specifically, which I know you asked for. I'll work on a RegEx for you as well, but these solutions seem simpler and lighter than full RegEx:
Pass the file names into the GetExtension method like so:
string extension = System.IO.Path.GetExtension(filename);
This will give you just the "002" or whateve the extension is, as long as you can pass in the file name (and not all of the extra "stuff" in the above lines.
If you can't isolate just the file name, why don't you just grab the last three characters of each line? That would get you the extension quite easily (unless the line doesn't end there).
To use RegEx to find these values, you would need to do something like this:
Match match = Regex.Match("05/25/12 06:34p 79 SysParaI.002", @"SysParaI.([0-9]{3})");
int fileNumber = Convert.ToInt32(match.Groups[1].Value);
This would find the three digits after the decimal where the file started with "SysParaI". It would find matches anywhere in your strings. I would only use this if you were looking for files inside a lot of text and couldn't predict where they would be. You would have to modify the RegEx to accomodate each file name (EqtParaI, EqtProgI, etc.) but this should be easy.