Current versions of Safari are able to access PDF documents in a number of different ways. It can display the documents inline (in the Web browser window) without the use of a plug-in, it can use the Adobe Preview plug-in to display documents inline with added controls, or it can pass PDF viewing duties off to another application like Adobe Reader or Apple's own Preview.app.
Unfortunately, the method used for display is not always the one desired by the user. There are several ways to control this behavior.
First, if it is present on your system, you can launch Adobe Reader (located in /Applications by default) and open its preferences (from the Adobe Reader menu). Go to the "Internet" section, and look at the options. If you would like Adobe Reader to launch when you access a PDF in your Web browser, place a checkmark next to "Display PDF in browser using:" and select Adobe Reader from the list.
If you would like to use the Adobe Preview plug-in, un-check the "Display PDF in browser using:" option, and place a check next to "Allow fast web view."
If your browser still insists on launching Adobe Reader when you would not like it to, navigate to /Library/Internet Plug-Ins/ and remove the following file:
Note that if you are using an Intel-based Mac and would like Adobe Reader to launch when you view PDF files in your browser, you may have to locate Safari application icon, click it, then perform a "Get Info" command (either from the "File" menu or via the Command-I keyboard combination) and select the option to "Open using Rosetta." This will significantly degrade speed, but allow the two applications to work properly together, both in PowerPC-mode.
If you would like to view PDFs using Safari's built-in mechanism, simply remove the aforementioned Adobe plug-in, and turn off the aforementioned options in Adobe Reader ("Display PDF in browser using:" and "Allow fast web view.") then quit and re-launch Safari.
Another alternative some users have found preferable is the use of Schubert, a third-party PDF browser plug-in that provides great flexibility and controls, and allows you to instantly open PDFs in Adobe Reader or Preview if need be,