My method is a big laborious but it can work pretty convincingly:
First off--use a computer based sequencer like Digital Performer (top choice IMHO for any MIDI sequencing *IF* you have a Mac) or Cubase (next best bet or best choice on PC).
Only program patterns that a drummer can physically play. Make sure each roll is different--even if the pattern is the same change the velocity on the hits somewhat.
Hit the entire MIDI track with subtle amounts of random velocity and timing randomization. Like maybe 1-2% on the timing, and maybe 8% on the velocity. Do this for EACH drum seperately. You probably want the kick and snare a little more steady than cymbals, high hats and toms.
Only choose *realistic* drum sounds. Ultra gated kicks that sound like your head being stomped on with a 20 ton elephant are no-no's.
Modify the sounds as well if you can. Don't use ultra common sounds like anything on an Alesis SR16.
Consider choosing two kicks and two snare sounds that are very similar or modifications of your main sound--as if you had "double miked" them. Remember these for later so you can apply some filters or other effects to "duplicate" the sound of a under snare mic, or mic that is on the beater side of the kick drum. Later on submix these into your primary kick and snare sounds as if you merged them in the mixer buss.
Imagine the drum kit playing the song and what components are in it. Where are they at? Draw a diagram if you have to. What types of cymbals do you need? Customize the samples to represent 3 or 4 cymbals and where they are located in the kit. Some of these may be just modified versions of the same cymbal elsewhere in the kit pitched up or down a bit, or eq'd a bit before mixing... DO THIS! It makes things more realistic. Try to give each cymbal it's own character.
Also, the biggest weakness of drum machines are the high hat and cymbals. Do your best to get them sounding realistic... also, human drummers put a LOT of emphasis on how they play their high hat. Make a number of different volume levels AND sustain/attack levels for different high hat "feels". Examples: totally closed high hat, partially open but still tight, partially open and trash, totally open 'mashing the oars', and something for high hat chokes. Also make sure that the high hat chokes correctly and doesn't trigger polyphonic samples--but only one sample at a time. Now use these feels where appropriate in the song. Change it around like a real drummer does. When combined with the random time/velocity you can make it pretty convincing.
Run each sound *INDIVIDUALLY* into a mixer as if they had been mic'd. Process them like normal drums... add a small touch of EQ to further modify the sounds from the stock samples. If you have to buss them in groups do them as: kick / snare / stereo toms / stereo overheads.
Once in your mixer create a fake "overhead" mix down. Put low levels of kick, some snare, high hat (in proper stereo pan), cymbals (stereo panned to taste--not too wide, about 30%), toms (stereo panned appropriately, like 15%ish) and so on. Make it sound a lot like overhead mics--plenty of bleed but in general a good 'snapshot' of the overall kit sound. Be careful with too much kick, toms or snare... you want the cymbals to be predominant. Definately apply reverb to this to give that sense of space. Use the BEST reverb you have available. Reverb will help hide the cymbals and high hat as best they can....
Now throw away the cymbal tracks.

If you want to do something to the cymbals modify the "overheads" like you would for real.
You would probably want a lot of seperation on the kick, snare and toms so don't use this trick with them. It will save you gating and so on. However, if you want to experiment with making these 'bleed' mixes and then going back and gating them a bit for added realism it can't hurt--it will add a lot of time though....
Anyways, mix down your toms into a stereo file so you can put stereo reverb, eq, compression on them like normal.
Now mix like you would a regular kit. For added realism do a submix of the entire drum kit and compress the snot out of it, mix this back in around -20db or so (i.e. "parallel compression"). Can add some beef.
Basically:
-program it realistically in the sequencer with human feel and personality
-set up the sounds to be realistic
-set yourself up to RECORD and MIX it like real drums
-then treat it like real drum as you mix it
If the high hat/cymals are a real pain you can always leave those out and do THOSE by hand. Set up some overhead mics and a high hat mic and play along with the song.
If you want a "room" sound, run a mix of the entire kit playing sans effects into a PA loudspeaker and turn it up to drummer volume levels in a decent sized, decent sounding room. Mic the room with some condensor mics however you want and record that. Treat those as your room mics and put them in your mix subtly. It will add that 'micro delay' that makes real drums sound realistic when recorded with microphones. Mix that in there at fairly low levels.
If you want a bit more realistic snare, run just the snare thru a monitor and MIC that.
Or do the old 'big speaker with a snare on it' using the snare track to trigger the speaker to vibrate the snare with each hit. Mic that and mix it in there.
Get creative. It can be a lot of fun. You can fool people with drum machines!