Is your check engine light on? When was the last time you did a tune-up (plugs,wires, air and fuel filter, pcv valve)?
Could be a vacuum leak. Check all your hoses and connections with carb cleaner. Also check around the UIM as they are known to crack.
Have you cleaned the MAF?
And no, I don't think it's a tranny issue. When my car had a massive vac. leak it would run great in Park and Neutral as well, but as soon as you put a load on it (i.e.- putting it in gear) the idle would suck and I would almost have to 2-foot it to keep it running.
Jay