I'm not sure that I understand your request. The script in my earlier reply (Re: join column 3 for unique values) will work with additional columns in the data file. For example, if data.txt contains this

A1 abc yellow 1 abc
B1 xyz green 2 def
A2 cde red 3 ghi
A1 abc green 4 jkl
A2 cde yellow 5 mno
A1 abc blue 6 pqr
[download]

the output will be

A1 abc yellow:green:blue 1:4:6 abc:jkl:pqr
A2 cde red:yellow 3:5 ghi:mno
B1 xyz green 2 def
[download]