Brian Walton
Jamstix. Big learning curve but when done right it can make AD or Superior sound legit.

+1 to this... but take note of my earlier comment regarding velocity curves. The jamstix internal sounds react differently at different velocities to AD2 (not tried Superior, but I suspect its the same).
 
Also, Jamstix does a clever thing with velocity/expression in its internal sounds to get a more random output. In other words, it might play velocity sample 64 at full volume, then for the same "hardness" of note play velocity sample 80 at a lower volume. AFAIK it doesn't do this when using MIDI mapping.
 
Bottom line is, if you're Jamstix / AD2 parts still sound like a drum machine, try tweaking your velocity curves.

I play it on midi keyboard or drum pads. It gets some humanity.

Lots of good info here.  I also start with the loops provided in EZ2 or AD2 as they are played by actual drummers and are infinitely better than me trying to play high hats naturally on a keyboard. I'll often do fills by hand in the drum map.
 
 One thing that is especially important is to vary the tempo throughout the song to sound natural.  Create a tempo map once your song and drum parts are laid out, BEFORE you start playing guitar or keys or whatever. Let the song breath into the chorus and speed up a bit etc. 
 
Once I have that, I play all the instruments to the drums.  Last tweaks are to go in and manually adjust velocities of hits and things to make it all as natural as possible.

I use aerodrums with Superior Drummer 3
https://www.youtube.com/watch?v=CavlglPYVvQ
 
Looks weird, but the software actually works really well. I cant be bothered programming drums and having played drums myself this is much more efficient. 

There are a TON of great ideas here.  My thanks to everyone who weighed in.
 
Here are my 2 cents: bleed!  Midi drums are recorded one at a time, real drums are recorded as a kit.  The difference can be pretty obvious.  If your drums vst lets you control the amount of bleed try turning it up and see if that helps.
Secondly, is panning.  If you listen to real drums they aren't usually spread all over the stereo field, but are panned slightly from the center, so maybe try tighter panning.
 
Again, thanks to all you posters.

Now try and program a Steve Moore:
https://www.youtube.com/watch?v=ItZyaOlrb7E
 
For added realism, you can have the drummer get drunker through the track, drop his (/her) sticks several times; tell a few lewd jokes, slag off the bass player; Change tempo through the track (as mentioned above) ... but not in time with the rest of the band. Some of that you can do in AD2.
 

Andyjobson 85 good music.

Wow, great topic, hard to find something that wasn't previously covered here.
However, being you have AD 2, have you ever noodled around with the "Transform" functions?
 Open the "Beats" window and on the right side of the GUI click on the "Transform" tab and you have all the basic tool there to humanize loops, and even edit things you've previously sequenced yourself.
 Adjust velocity, accents, random timing, time signature, kit piece mix and resign pieces, and adjust the length of a loop a lot of good tools to experiment with

To repeat: JAMSTIX.

EDIT:
Just downloaded newest version of these and they are not the same. Will investigate. I still have saved exe's of the older versions I use now.
Been using mdi drums since the late 80's. Alesis drum machine was first one iirc.
Now I use ez drummer 2 and Steven Slate Platinum Drums 4 and, ready Franks Midi plugins. It's a suite of p-lugs for midi like none I have ever seen before. been using them for about 12 years, but only for drums.
You can demo them so worth a download Google Franks midi plugins.