Can I use Remote Desktop?

you can use VNC server to remote a windows 2000 server, or you can enable windows terminal services on windows 2000 in services.msc and use RDP after that

I use VNC alot - I find it more useful to 'see' what's happening at the console, rather than in a new session - BUT some people might argue VNC is less secure than RDP.  I'm not a security expert and my servers aren't publicly accessible - I've never had a problem with VNC.  UltraVnc offers an encryption plugin as well, although I'm not sure what level of security it really adds.

RDP works fine too and may give you some features VNC won't (ie.. printing to a local printer).

Both VNC and RDP have their uses.

I tend to use VNC since it is more lightweight and doesn't cause anything to slow the server down by initiating a TS user logon separate from the console logon. RDP is useful if you know an admin is using the console session of the server, or if you want to perform what you are doing in a separate user session to the console. The only other benefits of using RDP over VNC are when you need to be able to access the disk drives in the local computer (the one you're physically sitting at) from the remote machine, perhaps if you have drivers to download remotely from CD or something. You can achieve very similar behaviour with printers and by using the clipboard in an RDP session (you can't in VNC) too.

As for security I don't trust RDP or VNC encryption or security (particularly the free version of VNC which offers no encryption) and I would never open their ports up for internet access; I've heard too many stories of people breaking into them rather easily. Instead if you need to do remote control of the server, you're much better off setting up a simple PPTP VPN (which does much better encryption IMO anyway) to log in to the network from outside, then initiate an unsecured (or less secure) VNC or RDP session over that secure link.

http://www.realvnc.com/products/download.html - Free Version is usually sufficient

tigermatt has a good point - if you are looking to access the server over the internet, use a VPN - my comments above were assuming you wanted LAN access only.

logmein is another great free solution