I have a project that I want to run and debug on my linux server.
The linux server is linux 2.6.18 and it has no GUI.
The operating system I am running on my computer is windows xp.
What are my options so that I will be able to run/debug the project on the linux server using the eclipse GUI?
tnx in advance.

So you need VNC software, client part for Windows, server part for linux.
After installation and configuration you will be able to login on remote linux desktop (Aka windows remote desktop)

VNC is for GUI (OP said Linux box is command-line only).

Install gcc/gcc-c++ on the Linux box and compile/run from command-line. For debugging you can install gdb (make sure you include the -g option when compiling/linking). For Redhat systems use 'yum'. Debian is 'apt-get' (must have root password to run either of those). You can SSH to the server using a program like PuTTY. Transfer your source files via FTP or SCP, or simply copy/paste into vi editor.

http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html

http://www.google.co.uk/#hl=en&xhr=t&q=eclipse+AND+c%2B%2B+AND+%22remote+debugging%22