This is a difficult question to answer because different packages specialize in different aspects of web analytics, they employ different workflows, they allow different forms of integration and extension, and so on.
However, there is a fairly consistent series of features that any package must have to be a top contender in general and to be considered by the vast majority of projects as their analytics provider. This list of features is rather long, but I'll argue that it must includes robust and flexible (and finely targetable) data collection devices, extensive and extendable reporting mechanisms, and a vibrant support infrastructure. With these in mind, I'd suggest that the top contenders are:
- Google Analytics: Free and so complete that it is enough (or more than enough) for the vast majority of websites (and many mobile apps) in almost every category.
- Kissmetrics : Professional analytics with a professional price (not the biggest price tag out there, but definitely not for tight budgets). Amazing support, highly actionable intel with minimal effort; truly a massive bang for the buck.
- Piwik : Very similar to GA in many ways, but hosted on your own server. This is very appropriate for projects that must fully control their own data, but potentially significant technical overhead should be expected.
MozPro and SEMrush both offer a great deal more than "simply" complete web analytics, and are often used in conjunction with other packages.
There are, of course, other analytics packages. But of the packages I know, these are the one's I think of whenever we talk about what's "best".