What is the standard way to analyze EEG data in a mismatch negativity paradigm? I'm running an EEG experiment using a modified auditory mismatch negativity (MMN) design, and I'm wondering if anyone can tell me the best method for data analysis (and recommend any stats programs/packages for this purpose as well).  

The experiment will only have a few (6-8) subjects with a high number of trials per subject (~700).  The matched condition makes up 75% of the trials.  The stimuli are selected from a closed set of 10 items, with an equal frequency of items in the matched/mismatched conditions.

One of the differences between this study and normal auditory MMN tasks is that the expected/unexpected stimuli vary between trials with the expectation set up on a trial-by-trial basis.  Therefore, it's possible that the difference in event-related potentials (ERPs) to expected/unexpected stimuli will be averaged out due to small variations in response to these changing stimuli.  

Does someone out there know the best EEG data processing and analysis techniques to detect the small ERP in response to auditory MMN stimuli?  Can anyone recommend techniques to avoid averaging out small ERPs whose latencies might vary?
Programs/packages for EEG analysis
There are decent MatLab toolboxes with good tutorials for for the analysis of EEG data. The EEGLAB toolbox (tutorial) can be operated by both GUI and command-line (and script). The fieldtrip toolbox (tutorial) is mainly operated by command line / script. 

Of course there are also (commercial) software packages for EEG analysis that do not require Matlab (e.g., BESA, Brain Vision Analyser, eeprobe), but I am not familiar with them. 

Are there techniques to avoid averaging out small ERPs whose latencies might vary?
No, probably not. ERPs are calculated by averaging across multiple trials because this averaging cancels out all components that jitter in time (that is, mostly noise), i.e. the thing you want to avoid (canceling out of jittering components) is actually the purpose of calculating ERPs.

However, to be sure you should have a look at reviews or tutorials for the measurement of the mismatch negativity. See for instance

Duncan CC, Barry RJ, Connolly JF, Fischer C, Michie PT, Näätänen R, Polich J, Reinvang I, Van Petten C. (2009) Event-related potentials in clinical research: guidelines for eliciting, recording, and quantifying mismatch negativity, P300, and N400. Clin Neurophysiol. 120(11):1883-908.  (pubmed)