Jack the Giant Killer really ends up being the best overall. That boost to HP and MP will really help against the bosses.
Everything else had such a minor bonus that it really didn't help much but I would go for the one that improves capture rate or item drop rate.
I wouldn't bother with the EXP bonus until the end. If you are going for trophies you will spend a lot of time grinding enemies for items and you will easily level up your familiars long before you collect all of the items needed.