I recently discovered this excellent video (see bottom of post) of all-round awesome Annie Sakamoto performing muscle ups in slow motion at the 2011 CF Games. There are many styles of muscle up technique now practiced, Annie has more of a classical "pull" style which is the same one I typically employ under fatigue.
Watching the video has validated the training advice I give to people who are learning the muscle up or are looking to improve their rep numbers in it - practice hard ring rows (with/without false grip) and deep dips.
I once heard a gymnastics coach describe the muscle up as "the highest pull-up you've ever done into the lowest dip you've ever done". This does describe some muscle up variations quite well (i.e. the stricter forms), however you can clearly see that Annie isn't really performing a pull-up in the usual sense of the word.
For Annie, the real "pull" motion occurs with the body virtually parallel to the ground (i.e. not vertically positioned) which is "rowing" strength and power as opposed to pullup strength and power. Once she flips her shoulders forward though, the dip position she achieves is VERY deep - note that the upper arms are well below the top of the rings... (also influenced by the size of her arms - Annie is not the tallest athlete).
As you get fatigued and height of pull decreases, the only thing that will save your muscle up is fast action forward and strength from a low dip position. It is worthwhile then to really extend the depth of your ring dips when practicing for muscle ups. A drill that is particularly useful is repeatedly lowering into the deepest dip you can control and practicing letting the rings drift slightly away from your body and then drawing them back in before pressing back up to full arm extension. Only perform this if you are strong in ring dips and have healthy shoulders.
The other video links in the youtube sidebar (all from user "hookgrip") show some of the other women performing muscle ups also. There are variations in technique which typically involve different lowering strategies and size of kip. Depending on the technique used, the dip may be as low as Annie's or may also be higher but all of the women pass through the parallel or close to parallel body position and therefore are pulling in a "rowing-horizontal" direction.
So the short advice is - if you employ a "pull" technique similar to Annie, invest some time in getting some ring rows done (make them hard - 4-6 reps max) and work a very deep dip and some ring holds in the bottom dip position. Your muscle up numbers will soon improve and you will save more reps that you may have lost before!