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Should i go with Microsoft or Linux OS, since my backbone is going to be running Novell

Depends on the admin tool support. One of our NetWare admins runs Linux but he needs to keep Win2K in VMWare for some of the tools as they either don't work at all (mostly just the older stuff like nwadmin for the older servers) or they don't work quite right (I think the DHCP plugin was one that didn't work quite right, but don't quote me on that). The new stuff is almost all Java so it can be made to work with a little work, it all depends on how persistent you are =)

The main consideration to think about is "can I do everything I need to". This includes things like reading mail too, because there's no free Exchange client for Linux and I have no idea about Novell's mail stuff. If you're setting up the mail stuff too you could just enable IMAP and use that, but it depends on what you want/need.
 
Just so you know, if you need a linux exchange client you can get Ximain's evolution (which is free) and add Ximian's connector to it ($70 for a single liscence, different corporate pricing structures though)...

Either way, I won't use either Linux or Windows clients untill I get either one of into a back room somewhere and test it.

Since I don't have any experiance (other then windows in school) with either Windows or Linux while working with Novell stuff, I can't recommend anything. Of course my personal bias is towards Linux.
 
Better late than never? The answer is pretty clear. Go with Microsoft as an Administrative workstation.

Novell is trying to push their systems to Linux as a server OS, but is going to lag on the workstation support just as they are on the Macintosh. It's a Microsoft world and that's where the best administrative tools are still run. There is a version of ConsoleOne available for Linux, but I still prefer NWAdmin for some things.

NW6.5 will be moving a lot of things to the web since they introduced iManager 2.0 with it. Be sure to check out the extended configurations you can do with it to provide only the services you need with organizational roles. (they work better than they used to)
 
You can make a pretty easy transition from NDS to ActiveDirectory on the high end. Actually most things are really simple to do in XP/2000/2003 so it's easy to ramp up to speed quickly and get things done in MS if you already have the core concepts down from running some other NOS. Just having good desktop experience with MS OS's will allow you to learn DHCP server in about 5 minutes if you've done it elsewhere. Keep the job market in mind as well. Jumping from Novell is definately a good move, it's a slowly sinking ship. Linux is a nice OS but it's going to be a long time yet until it dominates Microsoft in the job market (if ever). Linux -vs- MS can become a religious debate between zealots so my advice is to ignore anyone who is 100% one way or the other. If they can't recognize the merits of the other side they're not worth listening to. You've heard my $0.02 in favor of Microsoft, I'd recommend nothinman above for opinions regarding Linux. He's probably the most knowledgeable non-zealot I know of.
 
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