As pointed out in the other answers, Linux was meant as a multi-user from day one, so there's no problem with multiple users working simultaneously. Just give every user their own login account, then they'll automatically get their own home directory, and can work independently. Both VNC and NX will work for remote access. You can even use Linux as an RPD (Remote desktop protocol) server, if you want to access it using Windows's built-in RDP client (no experience with that though).
One point to note: You write
but when one user run the project from eclipse then he can but other user cann't run that project
Could you post the exact error message? "other user cann't run" isn't terribly helpful.
I suspect you are using a fixed TCP port for your webb application. While most resources on a Linux system exist per user, TCP ports are a global resource, so two users cannot use the same port simultaneously. You will simply have to make a rule so that every dev has their own port (one might use 9000, the next 9001, etc.). Then each can run the webapp on their own port (by setting it in the app server) without interference from others.
Note that running on a different port should make no difference whatsoever to a web app. While HTTP normally usees port 80, it will work over any port. Just access it as http://localhost:9000 (for port 9000) etc.