I'm new to optics and an looking for some sort of guide - like what goes type of scope for certain usages, what is mil-dot, etc...  I built my first AR15 with a flat top receiver from Fulton Armory and a Colt HBAR 20" barrel, full floating and need to compliment it with a scope but have no idea what to get!

A good quality set-up that won't be outrageously expensive, not complicated, but give great service, would be a Nikon "Pro Staff" 3-9x40mm in a Larue mount.

As far as learning about the various ins and outs of optics, all I can say is to simply cruise the forum here, and TRY to keep an open mind. If you chance upon a thread with any sort of pissing contest going on, leave the thread.

+1 on Zardoz's comments.  Folks can be very polar when it comes to optics so take opinions for what they are.  I would also suggest checking out different manufacturer's websites as they tend to have some good general optics info as well.  

Short answer to your Mil Dot question - it is a ranging reticle using miliradians (the "mil" in mil dot) as a means of estimating range to target based on the size of what you intend to hit.  Premier Reticles' website (www.premierreticles.com) has an excellent explanation of this reticle type, as well as decent prices (and great service) on Leupold scopes.  

As far as what type of scope for different applications, you'll get a lot of opinions on that one.  My eye sight is not that great, and I think that higher magnification helps my confidence on 200+ yd shots, so I tend to lean towards a max magnification of 14x.  I also like variable magnification because I typically use my rifles for target shooting and hunting so being able to dial down to 4 or 5x magnification is of some value to me.  For others, the simplicity of fixed magnifcation is preferable, or, they may shoot at very long distances and have no need for lower magnification.  I guess the point I'm making here is that are no hard and fast rules - some general guidelines maybe, but it is all about personal preference.  Some things I would consider before I make an optics purchase are - your budget, distances you will typically shoot, max distance you ever plan on shooting, intended targets (paper, tin cans, animals), and size/weight and how that impacts the utility of your rifle.

Take your time and do a lot of research.  It is a purchase that you will have to live with every time you shoot your rifle.  Also, plan on spending a few bucks on decent rings.

Hope that helps.

Thanks guys for the help!

I have another very basic question - 3-9x40 - is that 3-9 power magnification and a 40mm reticle?

3-9 power is correct.  The 40mm refers to the objective lens size.