Novice interconnect question.

If buying interconnects for a system comprised of a preamp, amp and CD player which link deserves the better quality cable. Finances limit my purchas to one good pair at this time.
If I understand you correctly, 
The one to interconnect will best serve you when connected between the Pre and Power Amp's.
My experience is the same as uru975 & F1's. If you're going to only buy one pair, start with the source. 
Depending on what your budget is for one good IC then start with the source to pre-amp.  If things get bottle-necked from the source the rest will be hamstrung.  If your budget is say, $300 for one pair then I would suggest doing two decent pairs of ICs from the likes of Audio Art Cables, Signal Cable or Audio Envy for that $300.  Two pairs of their budget lines will be a good starting point with minimal losses.  They all offer level up products that can be purchased at a later date and offer better performance.  Best part is they offer a money back trial period.