3) Everything is not exactly the same, or, use the appropriate installer for the platform.
If you're building the installer for a Mac OS X application, use a disk image for drag and drop, or an Apple installer. For Windows, you should use MSI, or whatever the follow-on for that is.
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This isn't just platform snobbery, it's a critical issue for sysadmins. When you use some third-party installer that essentially requires you to manually install everything, you make it really hard to install on a couple hundred machines. If you simply must use some bizarro installer, then please, please give us a way to install it onto multiple machines at once.
For example, starting with CS 2, Adobe added a way to do installs on Macs completely via the command line. This was a nice workaround for their insistence on not using the Apple installer.
Microsoft, while making the initial install for Office 2004 simple, then messes it up by making it really tedious to install updates. Adobe is starting to move towards the whole "installer downloads the installer" thing, and even worse, the downloaded files are opaque to most of the sysadmin tools on the Mac, which means you have to figure out what goes where to build your own installer. Gah.
4) Think of how someone will install your application on a couple hundred machines in different locations.
Just because it "only requires a few clicks," that doesn't make it a great install process for a couple hundred machines. If I have to manually install it, or build my own installer to install it, the installer stinks. Period.
Ideally, use either drag and drop or an Apple installer. Barring that, give me a way to customize the manual process. In other words, do the work so that I, the person installing your application, don't hate your product.
Apple used to make me scream with the QuickTime updates that made you watch the "GET PRO NOW" message half way through the install. Luckily, the sound of millions of voices crying out made them stop.
Another part of this is don't force me to install it in /Applications. Just because you think it's the best place has no bearing on anything. Schools, labs, and corporations all have specific procedures for installing things, and it is your job to be flexible here. Dont make us do silly workarounds like symlinks back to /Applications just because you don't want to do the extra work of adding some flexibility into your installer. Software vendors disagree on this.