I have a dedicated desktop machine that runs a linux game server that needs to handle at most a couple hundred users. I currently have a 50/50 Mbps fiber line for internet connection and am trying to remove any bottlenecks. My primary concern at the moment is the onboard NIC that ethtool states runs at 100Mb/s.
My question is: Is there any reason I should upgrade to a better NIC?
Consider getting a server-grade network adapter (examples).
They can possess their own processors and specific/faster logic systems to make for better off-loaders which will free up the system CPU(s) from processing network traffic.
Many newer ones are multi-processor aware (for spreading load and directing traffic to threads) and optimized for virtualization hosting.
That's why they exist, and why they're not as cheap as the $15 Boobophonix desktop adapter available at the local Rat Shack. ;)
Since your Internet is 50/50Mbit at best, a 100Mb card should do fine, so you may be able to find an older server-grade card on-line for a good deal.
Since, as you state, your net connection does not exceed 50mbps in either direction, and your NIC card operates at 100mbps in either direction, you have bandwidth to spare at the NIC. It is not the source of your bottleneck, so there is no pressing need to upgrade your NIC.
If you did upgrade your NIC, unless you purchased a gigabit NIC like THIS you would still be purchasing a NIC operating at 100mbps in either direction... just like the one you have. If you did purchase a gigabit NIC, you would also have to purchase a gigabit router to connect it to, in order to have faster than 100mbps between you and the router. But... purchasing a gigabit NIC and Router would not increase your net speed, since you only have 50mbps upload. You could theoretically operate the server with a Wireless G Nic, at 54mbps and still provide just as fast of a connection.
If you are having 100 people connect, your biggest potential bottlenecks are the amount of Ram, the speed of your processor and the number of cores/threads.
