You can have your character and/or your henchmen work at a job if you/they have equal or more skill points.
You can also earn money by:
Putting stuff up for auction.
Take out a Loan at the bank.
Loans
Here you can take out loansto a maximum of 20000 zeni, but you have to pay it back within 3 weeks plus 100 zeni or the bank will take all of your money and items to equal your payment.