Command-line-wise, almost none, although this has been changing (for better or worse). Linux has a much larger market appeal and following than any commercial UNIX. GUI-wise there are also no major differences--Linux, as most other UNIXes, uses an X-Windowing system.
The major differences:
Linux is free, while many UNICES (this is supposed to be the plural of UNIX), are very expensive. The same for applications--many good applications are available on Linux free. Even the same commercial application (if you wanted to buy one) typically costs much more for a commercial UNIX than for Linux.
Linux runs on many hardware platforms, the commodity Intel-x86/IBM-spec personal computers being the most prominent. In contrast, a typical UNIX is proprietary-hardware-bonded (and this hardware tends to be much more expensive than a typical PC clone).
With Linux, you are in charge of your computer, whereas on most UNICES you are typically confined to be an "l-user" (some administrators pronounce it "loser").
Linux feels very much like DOS/Win in the late 80s/90s, but is much sturdier and richer, while a typical UNIX account feels like a mainframe from the 60s/70s.
Some UNICES may be more mature in certain areas (for example, security, some engineering applications, better support of cutting-edge hardware). Linux is more for the average Joe who wants to run his own server or engineering workstation.
What are the differences between Linux and MS Windows
Mouse-click-wise, almost none, once Linux is properly installed. Linux installation can be a challenge though, whereas MS Windows comes, most likely, pre-installed with your computer.
The major differences:
Linux is free, whereas MS Windows costs money. Same for applications. If MS Windows or Office comes preinstalled with the computer it is unlikely it is free. Ask in the store to take it off your computer (your run Linux) and you are likely to obtain a discount, at least in smaller stores.
Linux file formats are free, so you can access them in a variety of ways. On MS Windows, the common practice is to make you lock your own data in secret formats that can only be accessed with tools leased to you at the vendor's price. How corrupt (or incompetent?) must be the politicians who lock our public records into these formats! "What we will get with Microsoft is a three-year lease on a health record we need to keep for 100 years" [http://news.bbc.co.uk/hi/english/health/newsid_1694000/1694372.stm].
With Linux, you are unlikely to violate any licence agreement--all the software is happily yours. With MS Windows you likely already violate all kinds of licenses and you could be pronounced a computer pirate if only a smart lawyer was after you (don't worry, most likely none is after you).
MS Windows tries to be the "lowest-common-denominator" operating system (for better or worse), whereas Linux is built for more sophisticated, feature-hungry computer users (for better or worse).
MS Windows is based on DOS; Linux is based on UNIX. MS Windows Graphical User Interface (GUI) is based on Microsoft-owned specifications. Linux GUI is based on an industry-standard network-transparent X-Windowing system.
Linux beats Windows hands down on network features, as a development platform, in data processing capabilities, and as a scientific workstation. MS Windows desktop has a more polished appearance, smoother general business applications, and many more games for kids (these are not better games though--Linux games tend to be more sophisticated).
Linux is more feature-rich than you could imagine. Heard on the Internet: "Two big products came from the University of California: UNIX and LSD. And I don't think it's a coincidence." MS Windows is simpler.