I have a 2003 subaru baja (automatic) and have recently been experiencing what I believe to be a transmission problem. When in idle the car vibrates more than when in park or neutral. 

Also, when I come to a complete stop after driving for a bit the car has problems accelerating. It will stutter in between gears. I alleviate this issue by letting off the gas then trying to accelerate again. When this happens there isnt any distinct noise, the only thing that happens is the car shakes. 

Any guess on what I might be experiencing?

Two things come to mind. I have the same rig and it did/does the same thing. When is the last time you had the filters changed and the tranny flushed? When mine started doing it a few years ago, I did both and added some Trans-X. I'm a driveabilty tech at a dealership, so I did it myself. It lessened the problem, but it's still there, just not as noticeable. The consensus between myself and our tranny guy is that I have a valve body issue of some kind. Since I've got 150K on it, I'm leaving well enough alone until it warrants pulling for and overhaul.

first item sounds like aftermarket axles - search,- well known problem. I suppose it's possible a worn original axle 'could' do it too.

what's the history of repair/maintenance on the axles and transmission?  

if the axles are aftermarket then that is a likely starting point to look into.

 

at first it sounds like:

1. axles - specifically the front inner DOJ joint

or

2. front differential

 

change the differential fluid and look for chunks or silver in the gear oil.

 

are the axles original?

ever been rebooted?

transmission fluid ever been changed?
differential fluid ever been changed?