Sounds like it's engine (i.e. fuel/combustion) shutter/stutter than mechanical. If mechanical, I'd start by looking at engine mount and asking when clutch was last replaced and/or bled.
For engine though, I'll start by asking if you recently replaced or disconnected the battery? If so, could be simply the DME relearning.
If not, I assume you're not getting a CEL light? If you are, go to local parts store and have them read the code.
Otherwise, I'd start by cleaning the MAF, throttle body and throttle control valve. Also, check your air fliter. By some chance something big may have gotten sucked in and is restricting the flow.
Tell us more symptoms so we can point to better diagnosis
