I use a budgeting program called You Need A Budget. It's an excellent program based off the traditional paper-envelope method. It integrates smart-phone access through an app and uses Dropbox to sync. Normally I wouldn't recommend products online, but I will do so happily for this company, as they have been incredibly responsive and helpful in addition to having a very useful product.
It avoids the pitfalls of classical budgeting in a few different ways.
First, it only uses your current money. It doesn't make you predict where or when your income will come. It has you assign the money to different user-created virtual envelopes. As you spend money, you withdraw it out of those envelopes.
This has a few benefits. It provides a significantly more accurate picture of your total assets and your total debts. Second, it helps the user prioritize expenses. It's much easier to not spend money on eating out when you can look at the budget and see that if you spend money, you won't be able to afford rent. Traditional budgets do this to a degree, but are significantly less effective and prone to error. When your expected income doesn't materialize, you find yourself unable to afford things despite having properly budgeted and spent for the month.
The second big thing for me about this program is that it's extremely easy to shuffle the budget. Traditional budgets simply aren't flexible enough to accommodate rapid changes. This program is designed to encourage switching the budget around. It takes a bit to get used to, but it very effectively diminishes or eliminates the shame encouraged by traditional budgeting.
There's a lot else, too: they run regular classes on budgets and have a whole budgeting method built around the program. Their user forums are extremely helpful and their support almost always responds within hours. It is expensive, a one time fee of $60, but it can be used for as many computers, phones, and people as you want. There's a 30 day free trial, and as I discovered when I bought it, they will give you codes to keep that trial from expiring until you can afford it.
Like I said, I rarely recommend things online, but I will do so for this company. The program is extremely flexible and useful for all sorts of budgeting methods. What I do in this program I used to do almost exactly in a excel spreadsheet, but this places it in a much nicer format, with impressive analysis options and reconciliation ability.