I use YNAB, others use Mint or other free budget programs from their banks. I started using YNAB because I like the way it handles credit card transactions - my free budget program from my bank always double counted all my spending, once as a purchase and once as paying off the credit card. Also helps track the cards I have and when payments are due - couldn't keep all that straight without it.
I also like the way the actual budgeting part works, and it has helped me identify areas where we were spending too much money (other than moving money around so that bills got paid and everything else went into savings, I was not systematic about budgeting at all pre-YNAB). Anyway, things are definitely a lot more complicated when you are juggling multiple cards, esp. if you start buying gift cards etc. YNAB does cost money, but I don't think I could play this game without it.