JavaScript
function parseLine(line, index, lines) {
if (m = line.match(new RegExp('^(\\d+),(\\d+)[^#]+#.{6}(?!00)[^(]+\\((\\d+),(\\d+),(\\d+),(\\d*(?:\\.\\d*)?)'))) {
document.writeln(m[1] + ', ' + m[2] + '<br>' + m[3] + ', ' + m[4] + ', ' + m[5] + ', ' + m[6] + '<br><br>');
}
}
input =
"41,6: (255,255,255, 0) #FFFFFF00 srgba(255,255,255,0)\n" +
"42,6: (255,255,255, 0) #FFFFFF00 srgba(255,255,255,0)\n" +
"90,35: ( 77, 80, 12, 98) #4D500C62 srgba(77,80,12,0.384314)\n" +
"91,35: ( 95, 99, 13, 78) #5F630D4E srgba(95,99,13,0.305882)\n" +
"92,35: ( 96, 99, 31, 90) #60631F5A srgba(96,99,31,0.352941)\n" +
"93,35: (106,110, 14, 68) #6A6E0E44 srgba(106,110,14,0.266667)\n" +
"94,35: ( 95, 99, 13, 78) #5F630D4E srgba(95,99,13,0.305882)";
input.split(/\n/).forEach(parseLine);