For a while, I used a mouse with my laptop. Because I was dealing with some wrists issues, I had the buttons flipped so that the main clicking button was on the right side, and the "right click" button was actually on the left side. Over time, I lost the mouse and resumed using the trackpad.
What drove me nuts, however, was how my Microsoft Remote Desktop Connection connections still were programmed with the flipped buttons. Even though my trackpad on my Mac was now set back to the default arrangement, whenever I connected to a Windows machine, my buttons continued to be flipped. And since I connected to these particular Windows servers from different Macs, I had to keep flipping the right/left preference in Windows each time changed Macs.
Unfortunately, there's no evident way to reset your mouse button settings on a Mac laptop via the normal PreferencePane in System Preferences if you don't actually have a mouse attached. No mouse, no GUI.
I searched high and low for where that setting is kept so that I could reverse it, so my RDC connections would also be returned to normal too. For your information, the right/left mouse button configuration is configured in ~/Library/Preferences/ByHost/.GlobalPreferences.[yourMACaddress].plist. That's a hidden, binary-encoded plist that's unique to your Mac hardware, in your home folder.
To edit this file, you will need to convert it to XML using the plutil terminal command, then modify the structure using your favorite text editor. You could also just delete it and a new, default one will be created, but this is a big plist with lots of discrete preference settings. Or, you could use the Property List Editor.app included with Xcode. TextMate will also allow you to convert and edit the file accordingly.