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I am looking after a server that has 6GB of RAM. There is a JAVA binary running that is using 1.8GB RAM, but nothing else is using anything near that, but I am seeing a constant 85%+ usage of physical memory.

The other processes don't add up to the difference so where else can I see what is using the memory?

I've never seen this before...

UPDATE 1: During my research I have discovered that SQL server can use more memory than it shows it is using in Task Manager. My box is running MySQL so I am wondering if a similar thing happens here?

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Have you tried the sysinternals process explorer? –  kafka Jan 11 '13 at 16:29
Can you be more specific? Is the 85% consumed memory active memory or is the majority of it buffers? –  MDMarra Jan 11 '13 at 16:33
and to add to @MDMarra - what tool(s) are you using to come to this conclusion? –  TheCleaner Jan 11 '13 at 17:10
I'm using Process Explorer and that shows Physical Usage as 85%. Where do I see it as active or buffered? –  neildeadman Jan 14 '13 at 8:05
Generally. using as much memory as possible to buffer and speed stuff up is A Good Thing (TM), which Windows likes to do when there is free memory wasting money just sitting there... –  Oskar Duveborn Jan 31 '13 at 16:16
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Windows has a built-in tool for analysing memory usage called Resource Monitor, you can start it by executing resmon.exe. By navigating to the Memory tab you'll get a graphical representation of your memory usage as well as process-specific data.

If you require even more information there is a Microsoft Sysinternals utility called RAMMap - it will give you a lot more information on both total and process usages. You can download it from here.

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