I *just* had to do that for the very same reason. It is incredibly overwhelming at first, but the trick is to break it down and take it slowly..
First, I separated the G3s into piles:
one pile for "seasonal," what I knew were valentines, winter series, halloween and easter.
one pile just for babies (and Tiramisu).
one pile for what I knew of or assumed were original ponies (before I started collecting G3s): this list composed of Pinkie Pie I and II, Rainbow Dash I and II, Minty, etc.. but also things like Sky Wishes, Applejack, Spring Fever and Shenanigans that I knew were relatively early as well.
then I made another pile for ponies I remembered seeing in stores. (I was only actively collecting G3s from 2005-2006). This left me with a handfull of Friendship Ball releases, tons of Butterfly Island releases and a few Crystal Princess.
Last, I made one big pile for anything with a turning head that WASN'T core-7. I knew they could only be 2006 or 2007 releases.
That left me with just core-7 and G3.5.
From then on I used mostly two sites:
first I went through Silverfall's Ponytopia, looking at each style in each year. It was a little time consuming, but it helped me find all the names I'd forgotten long enough to mark them on my checklist and toss them in the keep or trade bins.
Silverfall's only goes through 2007, and some of the ponies are hard to find (like if they came with an accessory playset, for example). So I made a general rule that if I got through a year (or an obvious section, like unicorns) without finding a pony, I'd set it aside and check out the pose guide afterward.
Then I'd use Strawberry Reef's pose guide.
That got me through everything except the core 7 and the G3.5, so then I used this:
My Little Pony Rereleases Encyclopedia the encyclopedia of re-releases! amazingly helpful, it details which core 7 ponies have what minor differences such as glittery forehead vs non glitter, etc. I thought I'd have to post a plea for help trying to ID three almost identical Toola Roolas and with that site I found it almost right away.
Now, keep in mind when I did this I was going through at least 400 loose G3s. It worked great for my huge collection, but if you have a smallish collection it might work in your favor to just separate ponies according to pose and look them all up on the pose guide, since it shows every pony in that pose on the same page.