you should only choose one over the other for programing reasons really. alot of people will talk about security, tho a properly maintained windows machine is just as secure
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If you've primarily used Linux/Unix based hosting, many of the control panels styles you have gotten used to will not be the same on a windows based host.
The most notable difference will be with your sites dynamic content and database activity.
If you're doing a lot of MySQL, PHP, or CGI scripting on your Unix/Linux host and you switch to a windows based host, you may have to do review on all of your software in order to migrate things. You'll also probably need to switch from MySQL databases to MSSQL databases. This in itself would keep me from making the switch.
If you just run a simple site with no dynamic content, then you probably won't notice much difference.
From personal experience, I have found a well managed Linux/Unix server is considerably more stable than a windows server. Anyone who claims otherwise simply doesn't know how to use the tools available to them in order to keep their server stable.
Performance comparisons is a sticky area to get into. Unless you're running a high-profile site you won't notice much.
Security and programming issues aside, the most notable difference is PRICE.
Linux hosting is almost cheaper 99.9% of the time than the next comparable Windows type hosting.
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Ive used both. (Caldera eserver, redhat 7.X, windows 2000 server) platforms.
I find linux to be nice in many of the command line functions that are do-able.
Windows is far easier in many ways for the basic configuration(s). (Though both OS's get complex when complex things are done)
I only have a year or so of experience in Linux, so I am nowhere near as comfortable as I am with windows, having used it for the past 5 or 6 years or so after Amiga went bust.
Many operations in Linux are somewhat obscure, and documentation is difficult to find at times. Variants of linux are not always completely standard to each other, so it can cause occasional issues.
Newsgroups and message boards for Linux are populated by a LOT of extremely surly, childish, and arrogent overgrown children. The general attitude seems to be "If you can't fix it, RTFM, if that doesnt help, kill yourself because you are stupid"
Windows has a few (well known) security flaws and exploits that need to be patched, and software takes somewhat more horsepower, and it costs more money.
Support for win products (free webpages, newsgroups, etc) is a lot easier to find and people there are generally happier to help.
some MS software is junk (avoid exchange like the plague--its takes pretty much its own server and tons of resources) but much is excellent from companies other than MS.
Keep your win server patched and hotfixed, and you should be all set.
also--make the use of the best of both worlds...install PHP and Perl support on your winserver and use some great things out there.)
I find MS to just be so much easier to install, uninstall, maintain and deal with than my linux servers were.
I've been dealing with the same issues migrating a current site to another host, but some of the following are platform issues you may want to consider:
ASP: Win - Very Common Full ASP with vbscript, Linux - Uncommon Apache ASP (no vbscript)
JSP: Win - Very Rare, Linux - Uncommon
PHP: Win - Very Common, Linux - Very Common
CGI: Win - Very Common, Linux - Very Common
MS Access: Win - Very Common, Linux - None
MSSQL: Win - Common, Linux - None
mySQL: Win - Rare, Linux - Very Common
Multiple FTP: Win - Rare, Linux - Common
Subdomains: Win - Uncommon, Linux - Common
Control Panel: Win - Uncommon, Linux - Common
Price: Win slightly more expensive than Linux
Stability: Linux tends to be more stable than Win
Compatibility: Win tends to have more software available, but rare to find everything installed (such as JSP and mySQL).
Although a majority of these technologies are available on both platforms, they haven't typically been fully implemented across platforms. You'll need to evaluate your personal development needs and may be restricted to a certain platform because of it. Basically if you need something like vbscript, MS Access, or MSSQL, you'll probably need a Win platform, but if you need multiple ftp accounts, subdomains, JSP, or mySQL, it would be easier to find those on a Linux platform although you may find them on Win also.