I've been using PocketMoney from Catamount Software on and off for a long time. It's very powerful - but I always found that, unless I had a particularly urgent need for budgeting and tracking my spending, I was never motivated to keep up the effort. Every other program I've tried, including the ones I'm about to mention, feels like I've traded away some subset of PocketMoney's power.
Currently I'm using two different apps (yes, that does mean that I'm entering every transaction twice. I'm not sure how long I'm going to keep doing this). One app is fantastic for forecasting your cash flow down to the last cent and second, so that you know exactly how much money you'll have on hand at any given time.
The other app explicitly refuse to enable that kind of forecasting. Instead, it takes the approach that you should only ever make a budget for the money you already have on hand. If you have long-term goals, you can start to meet those goals by setting aside some of the money you have on hand, but you should never start playing with money you don't actually have yet.
The first app - the one that does the forecasting is MoneyWiz
It's fairly simple to use, but has almost all the functionality you'd expect to be able to track transactions on your accounts. Its best feature is the ability to set up recurring (eg, $x salary in to account 1 every fortnight, $y for a recurring doctor's visit every 3 weeks) and one-off (eg, need to buy a birthday present for mum on june 15) scheduled transactions and then generate a forecast. For instance, I'm in the middle of planning to move house - I used this just last night to check how different levels of rent would affect me, taking into account all the other bills and living expenses I already know about.
The iphone, ipad, and Mac versions of MoneyWiz all support all the features and they all sync together, but you have to pay for each version separately (5.99 each for iphone and ipad, 24.99 for Mac). It's possible to just get the iPhone version and do everything with that, but I find it handy to use the ipad or desktop version to be able to see more detail, especially when I'm looking at the forecast graphs.
The other one I'm trying out is You Need A Budget, or YNAB for short. It comes in Windows and Mac desktop versions, and has iPhone and Android mobile clients to support the desktop program. The mobile clients are free, but they only support a limited range of functions. You need to have paid for the desktop version to use them, and they're mostly designed for you to check your budget balances or enter a transaction. YNAB has a free 34 day trial, but after that it costs $60.
YNAB doesn't do forecasting; instead it focuses on having you figure out how much money you have *right now* and what you need that money to do before your next pay. They don't explicitly say this, but obviously they believe that once you're collecting the data about what you *have* been spending money on, you'll be more able to make decisions that support your goals in the future.
As well as giving you 34 days to try it out, they have a comprehensive series of videos (http://www.youneedabudget.com/support - look for "YNAB 4 Video Tutorials" on the right) and tutorials (http://www.youneedabudget.com/support/category/the-ynab-method) which don't just cover how to use the program, they aim to teach you how to think about budgeting.
If you're looking for help budgeting because you just don't know where the money goes, I recommend giving YNAB a go - after all, it's free to try for 34 days (and there's your first savings goal right there - have $60 on hand to pay for it at the end of those 34 days!). Take the time to watch some of their videos and sign up for their 9-day email course - Even if you don't end up paying for it, the information you'll get from the progam about your own spending, and from their courses about what to do next, will leave you much better able to make informed decisions about your spending.
If you have some idea of where your money goes but need better visibility into some of the trickier patches, MoneyWiz is probably a better choice. YNAB is aimed at helping you spend the money you have; MoneyWiz is much better at helping you plan what to do with the money you're going to get later.
Personally, I've always been *horrible* with money. It comes in, at some point later it runs out, and then there's a bit of a panic until the next payday. MoneyWiz has helped me a lot: because I was able to see ahead, I started having the panic weeks before the money ran out - which meant that the money ended up *not* running out. However, that's turned into a steady stream of just-scraped-through paydays. I don't end up in the same panic any more, but I do end up only *just* scraping through.
I've only been using YNAB for a few days, but the way it presents essentially the same information as MoneyWiz in a slightly different format, combined with their propaganda, have already made a difference in the way I'm thinking about budgeting.
I think I might need to keep using MoneyWiz for a few weeks (maybe even months) more to help me past one last tricky place - but as soon as I have a bit of a buffer (nb: thanks to MoneyWiz's excellent forecasts, I know to the day when that's going to be) I won't need to MoneyWiz's level of precision, and I'll probably switch to just using YNAB.