Homebrew has some pre-built binaries too. From the FAQ: "Homebrew does provide pre-compiled versions for some formula that take a long time to compile (such as Qt which can take many hours to build). These pre-compiled versions are referred to as bottles and are available at: http://sf.net/projects/machomebrew/files.
1. Name your package manager, and I can list the missing packages, or missing flags which have made my life a pain at some point in my career.
2. Yup, and the only way, should you need to set any flags.
3. True. Which is why it's nice that you can mount dmg's and install pkg's via the command line.
My biggest problems with the above:
1. Neither Homebrew nor MacPorts (nor fink, for that matter) has a complete set of relevant packages
2. Compilation from source is ridiculously slow.
3. Certain utilities are best installed from .dmg files instead, and it's a pain to remember which was installed which way.