Probably a lot more detail is needed to give a useful answer to your question. However, there are some issues not mentioned yet.
First, what is the budget for system administration and maintenance? Is there a budget for that at all? I do (volunteer) system administration for a couple of small human rights organisation (about the same size as yours). They are cash strapped and don't have the money to pay for a system administrator, or to contract for the work as needed. The rely on volunteers, and these are really hard to find. So, ask yourself what kind of expertise is available before you decide on a system. makes no sense to design a superb system when you have no one to keep it running.
Hardware is generally kind of uninteresting. I would go for wireless (RADIUS) for as many clients as possible, and don't buy unnecessary powerful PC's. Waste of money.
One system I build was based on Google Apps (Education license available for non-profits) for mail and remote access and a local NAS with LDAP that synchronises with Google. Create an account locally, a Google Apps account will be created automatically. Clients Windows XP / Windows 7. What makes this a good system is very low maintenance, easy deployment (everybody knows Gmail, etc) and good support for remote users. Office staff can deal with almost anything needed to keep the system running. For the NAS I used a Intel SS4200 NAS with 4Tb raw storage and installed a core version of Ebox (zentyal) on it for filesharing. LDAP and RADIUS. Web interface, office staff can deal with that.
The second system is a MS Small Business Server 2003 with about 12 clients. That works well, problem is you need someone who knows SBS, and can handle sysadmin tasks. (And no, in my experience most people working for non-profits can't handle that). Licenses for SBS (and Windows) can be purchased through the Microsoft program for non-profits. it's cheap, and the money should be no problem. Mail runs on the SBS server, remote acces to the office PC's too. be ware that security is a bitch in this setup. Much harder to keep it safe that the first system.
You say you want to run the website from the office. I have no idea why you would want to do that. It's a headache. If you go the Googel Apps way, use Blogger for a website (if simple is good enough) or create your own website with Joomla (host it somewhere) and handle authentication for your website through Google Apps.