How to print incremental count of occurrences of unique values in column 1

The standard trick for this kind of problem in Awk is to use an associative counter array:

awk '{ print $0 "\t" ++count[$1] }'

This counts the number of times the first word in each line has been seen. It's not quite what you're asking for, since

Apple_1   1      300
Apple_2   1      500
Apple_1   500    1500

would produce

Apple_1   1      300     1
Apple_2   1      500     1
Apple_1   500    1500    2

(the count for Apple_1 isn't reset when we see Apple_2), but if the input is sorted you'll be OK.

Otherwise you'd need to track a counter and last-seen key:

awk '{ if (word == $1) { counter++ } else { counter = 1; word = $1 }; print $0 "\t" counter }'