I've had multiple times that by using apt-get autoremove, my entire Ubuntu installation has been fubared. It is almost nicer how Windows and Mac apps ship with all the required libraries and functionality they need, and you don't have to worry about it (both as a developer and a user). Add to that the confusion where programming languages have their own package managers (should I use Python's easy_install or the .debs?) and there's even more of a mess.
I've never had any difficulties on my Mac or on Windows due to a lack of a package manager, but I have had problems using apt.
I don't understand, what advantages does using a package manager have over simply shipping an app with the libraries/programs it needs? Yeah, you save hard drive space, but with hundreds of gigabytes of data, is that even important?
I've been using Debian for years, and Ubuntu recently, but I had to look up autoremove; I've never used that apt-get feature. I have used autoclean, which is benign. It does sound like there are problems with autoremove that should be fixed, but for now why not just avoid that feature?
I think one advantage a package management system has is unified updates. The down side is that could cause problems when configuration file formats change. Gentoo tries to handle this by managing all config files in CVS, so you can diff different versions and merge them. Luckily, in reality, config file formats don't change all that often.
Am I missing something? I wish it did this, but unless something has changed recently it just gives you a tool for merging updates in (and doesn't store old revisions).
Be default dispatch-conf keeps a backup of your config files in /etc/config-archive. Optionally it can use rcs to track changes.
It's not just about space; say somebody finds a security exploit in a widely-used library. How many copies of (eg.) libpng do you have on your system? Can you depend on every program that uses it to put out an update?
Now just yesterday I had a problem with apt-get on Ubuntu installing a bogus version of (I think it was) Ruby Gems.