I am going to develop a web based point of sales system. It is going to be based on linux and php. Users will access it via internet and using browser as the tool.

Problem is if the web server is down? The user want to be still able to do their business locally and update the central database once the web server is up? What best solution can I do here? So is web the right way to go or should I just build some windows based application.

You can use desktop syncing applications like Microsoft's SyncToy, SyncBack etc or have a custom application developed.

Should i then fully develop using C# everything else.

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You're probably better to use something like Java if you want to build it yourself. Of course this could be done in php/mysql, but it seems a little awkward having to install a LAMP/WAMP system on each machine.
For the user to use this locally, when the internet is down, you'd need to ensure that the local db had a up-to-date data with regard to products/pricing.

How to develop in JAVA using eciplse? How about C# ?

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I would imagine anything that can run on your OS without too much fuss and can access remote sites.
The tech should have the ability to write to disk / store locally, eg xml / json / applet.

The thing with PHP/mysql is that it depends on configuring a web server and a load of other guff.

You have any experience with c#?

PHP/MySQL for the site on your server if fine though. You just need to allow programs and other sites to access it (securely).

Dear Diafol,
            Thank you for your help but I think for the offline mode the best is C# then.