Hmmm, thats a big, complex question. For me, its Remember the milk. The reasons why are that I have access to my lists, online, on my phone, iPad and even through WAP. the downsides of RTM are that the app & services do not offer subtasks, BUT it does offer location based sorting, tagging, etc. For me, I just need a simple list system that I can use online, offline, alerts and what I mentioned above.
I thinking the real answer is "it depends". Personally, I would think about what you really need the app to provide you ie. Subtasks, projects, syncing, etc. I then review apps based on that criteria. A few good ones are Toodledo, Remember the Milk, Things, Listingly.com.
Hope this helps.