Windows prior to Windows 98 operating system used to be single user single task type. For example Windows 3.1 and Windows 95 were single user single task operating system. Only one application window was running the thread in the background for those operating systems. When Windows 98 was released it turned out to be single user multi task operating system. Windows 2000 was the first Windows to bring multi user multi task type to OS. And Windows ME was single user multi task like Windows 98 but with more networking support.
After Windows XP onwards, operating system was capable of being a server and allows multi user multi task. Now every release of Windows is multi user and multi task. Considering the Windows has it's own platform and now they are not releasing the single user operating system anymore.
1. Kernel - The kernel of UNIX and Windows both are different. The way UNIX kernel handles errors, threads and process are completely different. It can manage multiple users at the same time more efficiently. In case of Windows, it handles the multiple users in rather different way with ticket system compared to UNIX kernel. Another set of difference is that you can build many UI types and desktops on UNIX. In case of Windows, you have only one option when it comes to UI. You also don't have much choices when it comes to error handling compared to UNIX in Windows.
2. Security - UNIX handles security over files, folder and user level much better. It also has resource specific control too. In case of Windows UAC is too shallow. Also virus can still come in despite having UAC.
3. Centralized Repository: Windows has centralized app repository with registry and control panel. In case of UNIX, there is no centralized issue, and application run on the basis of shortlink and resource. And it's easy to remove their files and it can be permanent as compared to Windows.
4. Run levels - Windows offer single run level for the resources. In case of UNIX you can have multiple and still able to work efficiently.
These are some of the common differences. You may find more on UNIX based operating system's architecture on James Bach's book.