SSH (using PuTTY for example) is, if you ask me, the best way to control the server. If you don't run graphical stuff the load is smaller, and you can do everything needed commandline-wise. It's fast, it's not difficult (if you just take the time learning, and you should, if it's important -- if it's not, why are you doing it?) and it's accessible from almost anywhere (no matter which OS you run). Using graphical forwarding (just program windows or the whole desktop) is a lot slower, creates unneeded load and so on..but enough lecturing.
I don't recommend running X at the server, and bringing the whole desktop over network is too heavy for maintenance use. Instead you can use X11 forwarding feature of SSH (PuTTY has a box somewhere to enable X11 forwarding, and in addition it must be configured at the server end too) and launch a program trough SSH and get it visible on your Windows desktop. This way you can use the tools you need (and don't need the whole desktop). Bad part is that Windows cannot naturally out-of-the-box handle X11 stuff, so you'll need to get extra software to enable that; as far as I know, most of it is commercial and not cheap.
Third option is to use something like Webmin which works trough browser interface; you'll just need to allow yourself to use it (try to keep it secure..I'd prefer SSH over this, but if it's what you really want and take the risk, it's your decicion) and then learn to use it. Webmin can control a lot of stuff at your server, but remember to configure it well before starting to use it. More information about webmin is..on the web, of course
