Well, for me it kind of depends on the crying. If it's crying like he's in pain, then I usually break down and give him some tylenol. I'm not a big fan of medication, but if it has been quite awhile I take pity on the poor guy. Otherwise, I do two things: If he is congested, I express some breastmilk, use a medicine dropper to squirt it up his nose, and then suction it out. He hates this, but it is the absolute best decongestant I have ever seen. And I find most of his misery when he has a cold is due to either not being able to nurse due to congestion, or getting woken up by his clogged nose. Second, I usually spend at least part of the night sleeping sitting upright while ds sleeps on me. This really seems to help him when he is sick. He gets the comfort of sleeping on mama, and also it keeps his head raised a bit.
Good luck - ds has only been sick twice in his 16 months, but it is the absolute worst when it happens!