You use "well" to change the topic or the tone of a conversation:

A: How are your classes going?

B: Not too well, to be honest. Calculus is kicking my butt.

A: Well, hang in there.

B: Yeah, I'll try. Hey, have you talked to Priscilla lately?

You can also use "well" to signal the end of a conversation. For example, you might say this after talking to someone who's just returned to work from maternity leave:

Well, it's nice to have you back.