There are two different pieces of software you will need for this project.
The ISE Project Navigator is used to build your project, assign the package pins, and generate the programming file. You do not use it to transfer the programming file to the digiboard.
You can download the ISE WebPACK (4.9 GB download/10.8 GB installed) at http://www.xilinx.com/. You want the"ISE Design Suite 13.3".
There are at least four ways to navigate to it. 1) From the main xilinx page, click on the "downloads" at the very top of the page. 2) Mouse over "Products" and select "Software and Design Tools". 3) Search ISE WebPACK Software, then choice the correct link from the list. Or, 4) click on the link provided above.
On the ISE Design Suite 13 page you will see inks to the the ISE Design Suite 13.3 Full Production Install for "All Platforms", "Full Windows Installer", and "Full Linux Installer". (If you are ask to take the ISE WebPack survey, answer the questions (hint: Spartan-3). At some point you will need to register (this is free).
From this point on, I am only referring to the window install. (I do not have a Linux system.) For Linux and Mac follow this link to Erin's software notes. Allow the website to install the 'Download Manager' from 'Akamai Technologies, Inc.' This downloads a tar archive. A number of programs can extract this archive. In the lab I downloaded a free tool "PeaZip" from Source Forge.
Extract the files into a folder. Run "xsetup.exe". A welcome screen open presents itself. Read the istructions. Then there are two license agreements to check. Then you will be able to select the edition to install--I recommend "ISE WebPACK". Accept the default installation options). Why not accept the default directory as well. I unclicked the "Import tool preferences..." Then let 'er rip.
Near the end of the install (89%), the install will need your attention again. Then Microsoft Visual C++ 2008 Redistributable will install. This requires more mouse clicks. WinPcap requires a few mouse clickes. Then there is the "Windows Logo Testing" warning, click "continue anyway".
Then the "Xilinx License Configuration Manager will open. Choose "Get Free WebPack License". Then another window opens and asks if yoiu would like ot "connect now". You will sign in again. Continue to navigate. Check the "ISE Design Suite: WebPACK License", then click "Generate Node-Locked Licenses. After more clickes you will get to "congratulations".
Xilinx also has versions for Linux, however I do not believe Digilent has Linux versions of the USB programming tool. I that case you would need to use the JTAG cable and program the Nexys board from the parallel port. You will be in unexplored territory.
As of 27 Oct 2011, the installed version is 13.3.
The Digilent Adept software suite. This is used to transfer the programming file to the digiboard.
You can download this from the Digilent Adept Software page. Select Adept 2.3. This downloads the file "DigilentAdept_v2-3-0.exe". Run the .exe file to install the program. A window will open promting you to select which compents to install. Accept the default (only Adept Application is checked). You may get a message "Microsoft Visual C++ Runtime 9.0 not installed. Download the from microsoft.com", if you do, click "yes". The install may also complain "Xilinx ISE install not found", ignor this. At the end you will be ask to reboot your computer or to reboot manually later.
Notes on using Digilent Adept. After installing the Adept, connect your board to the computer using the USB cable. You computer will probably say "found new hardware". Allow it to install automatically. When this is complete, start Adept (Digilent>Adept>Adept). Adept should autodetect the USB device (this is the default), e.g. Connect: "Onboard USB", product: "Nexys - 200". If it doesn't, make sure the the power switch on your Nexys board is in the "on" position.