What are some of best tracking software packages available for PPC and a website?
The best can depend on what sort of PPC you are doing. I've used a few different solutions and can recommend a few for different types of campaign.
Google Analytics is my default website analytic package, it also integrates well with Adwords for smaller Adwords PPC campaigns.
For search PPC on Adwords, Bing, Yahoo, etc then you can try using Prosper202. It's free, selfhosted and easy to install and configure. A new version is due out "soon" with extra functionality.
I've not used it much but another good option is Bevo Media. It's got some more advanced features over Prosper202 however it's slightly more focused towards CPA and affiliate marketing.
If you're planning a campaign using CPV/PPV traffic then a more specialist tracking solution is CPVLab. Very powerful and flexible system that can track many different types of advertising campaigns.
For large scale display and media buys then you're going to be looking at a proper ad server. OpenX is free but does have some limitations. If you have a large budget then systems Google Doubleclick, Adshuffle and many more enterprise scale platforms are available but that's well outside my expertise.
I developed w3roi, which is a PPC ad tracking service with a 30 day money back guarantee, so it's essentially free to try.