Sometimes you don't feel very well, but you're not really ill. Here are some common expressions that you can use to describe general "aches and pains" and some useful "sympathetic" responses.
General aches and pains
"I feel a bit under the weather."
"I'm not feeling very well."
"I think I'm going down with a cold. I've got a sore throat."
"I've got a slight headache." (Or toothache / stomach ache / backache) Pronounced "ake" as in "cake".
"I'm not sleeping very well at the moment."
"I feel a little faint."
"I've got a nagging pain in my shoulder." (nagging = a pain that won't go away)
"I've got a splitting headache – I hope it's not a migraine."
"I'm sorry to hear that."
"You don't look very well."
"You look a little pale."
"Maybe you're going down with something. There's a bug going around."
"Maybe you should go home and get some rest."
"Why don't you go home and have a lie-down."
"I have a bit of a stomach bug."
"I think I've got a bit of a temperature."
"I have a touch of flu." (Flu = influenza)
"I've got a nasty cough." (pronounced "coff")