Most people today install 50 micron laser optimized fiber in the data center. It will support 10 gigabit and is fully backwards compatible with other multimode connections. Fiber equipment is more expensive than copper, so you will want to weigh each connection on its own merit. The best way to install it would be run all fiber from your main (core) switch to a fiber cross connect, the same for your switches. This allows you to connect anything to anything via a fiber jumper (patch cord) and allows you to utilize all your fiber ports on your switches rather than having to run a bunch of fiber all over the data center. Make sure you clearly label each end of each fiber just as you would copper.
This was first published in March 2006