I am no master on monster crafting but I'll take a shot at it.
For NPCs like these, I think the best solution would be to tack on a few more levels of their current class.
For example, currently you have a goblin warrior at level 1 and you wish to bump up his challenge rating. You could tack on another 2 levels of warrior to promote a lowly goblin grunt to a sergeant and he'd get all that would entail. Which means much more hit die, more BAB, more skills, a feat, and better saves. This would bump him up to a Challenge Rating of 1 (+2 of 1/3)
After that, you should upgrade his gear to match his new CR and status as Sergeant of his tribe. Masterwork weapon, breastplate, and a few vials of alchemist bombs for those pesky high AC fighters should make for an enhanced challenge.