Only a thought - maybe this is the A/C compressor kicking in as they cycle on and off to save fuel. It is more noticeable on a 4 cylinder engine than a 6 or 8, but I haven't really noticed it on my cube. It is somewhat noticeable on my wife's Honda Element, but I still wouldn't describe it as a shudder, just a quick minor drop in engine speed for a second. Not much help, but if it is consistant, a good mechanic should be able to easily diagnose it. Good luck.
2010 Scarlet Red Cube SL - Mine
2008 Orange Honda Element - Wife's
1978 Honda CB450A - Mine