I thought the community might appreciate some links, all posted in one topic, to sites which provide programs or features to enhance your server. If I've missed any feel free to reply and I'll edit the master list.
1. PsychoStats2: Great stats proggy with terrific support. Mysql db required.
2. AMX Mod X: A final release, it is a versatile Half-Life metamod plugin which is targetted toward server administration. It has a wide array of scripting capabilities so people can write "plugins", or files which add on to a mod's functionality.
3. Admin Mod: A Metamod plugin that allows you to administer your Half-Life server while playing the game from your client console. Multiple administrators with different permissions can be set up. Not nearly as popular in the NS community as the above, nor as customizeable.
4. modNS.org Forums: A wonderful community where you can download and discuss various AdminMod, AMX/X, and Metamod plugins.
5. Brys NS Maps: A super collection of custom maps and more.
6. HLSW: Server monitoring tool, a must have.
7. Metamod: Required if you want to run administrative, anti-cheat, or bot programs on your server.
8. RCBots: Marine and alien artificial intelligence bots.
9. Whichbot: Aliens only artificial intelligence bots.
10. United Admins Cheating Death: Cheating Death is what you need as NS has no VAC support.
11. WS_FTP95: An exceptional tool for uploading files to your server, AND it's free!
12. AdminOP: EntMod, HookMod, RadioMod - Half-Life server-side modifications.
13. ServerDoc: Will start a program and check the program is still running every five seconds (default) and restart the program if required (if its crashed or closed) on Win95/98/2000/ME/NT & XP systems.
14. FireDaemon: A utility that allows you to install and run virtually any native Win32 application or script (eg. BAT/CMD, Perl, Java, Python, TCL/TK) as a Windows NT, 2000, XP, 2003 & Longhorn service. Often used to restart crashed Windows servers.
15. HLDS Guides for Newbies by Vadakill: A well written tutorial on Half-Life Dedicated Servers.
16. Clanmod: A tool for Half-Life modifications like Counter-Strike, Day of Defeat, Natural Selection, or Team Fortress Classic which helps to administrate your server with minimal usage of console commands.
17. RCON and Natural-Selection CVAR Guide: An excellent reference written by Bry.
18. Steam Game Server Status Monitor: An innovative tool for Steam game server administrators. It is an independent software application which specializes in individual server monitoring for Steam Powered game servers.
19. HiveMinD: Alien AI for Natural Selection. *no longer supported: 09-23-06*
20. Steam Forums: Windows Dedicated Server
21. Steam Forums: Linux Dedicated Server
22. Mods Maps & Models for NS An alternative to modNS.org featuring plugins, maps, models, and more for NS. (currently redirected)
23. Tweaks To Win32 HLDS Tweaks affecting performance on the level of HLDS' player interpolation by increasing uninterrupted work time done by the server, and thus producing apparent smoother player actions.
24. number-7.com The Premier Natural Selection Custom Map Archive.
25. Outpost Firewall Free basic firewall protection.
26. HackerWatch Anti-Hacker Community: Simple probes and port scans.
27. #nsserver on Gamesurge.net: Live support via IRC for Windows and Linux server ops.