I'd recommend using environmentally friendly products that don't have fragrance and no strong chemicals.
For poop stains, I use OXO Brite by Earth Friendly Products (http://www.ecos.com/pages/oxo.html). This has worked great. I rinse the poop out as best as I can. Then I fill a sink or bowl with a scoop of OXO Brite. I rub out as much of the stain in that mix, then let it soak overnight. Then I wash the item with regular laundry (sometimes adding OXO Brite to the wash as well). Somtimes if I have several stained items, I'll do this process in the washer.
I've also used Bac-Out Stain & Odor Eliminator by BioKleen (http://biokleenhome.com/products/household/general), more so for cat messes on the carpet but it probably would work well for baby poop too. Probably best to spray on immediately after item is stained.
Another product I highly recommend is Dr. Bronner's Magic Pure Castille peppermint liquid soap (http://www.drbronner.com/DBMS/LS.htm). The packaging is a bit wacky, but this stuff works well on hard to remove stains.
I wanted to stamp my baby's handprint on a card and unfortunately didn't realize how bad the ink stained. So her little hand was all green, plus MY fingers. On my hands I tried using regular soap, dishwashing liquid, rubbing alcohol, nail polish remover, my husband's Lava soap - with no luck! Then I remembered I had the Dr. Bronner's. This took the stain off my hands easily with little scrubbing, so I used this on my baby's hand too. Whew I was relieved. I've also used it on blood stains on clothing with pretty good results.
The OXO Brite and Dr. Bronner's soap are usually sold at Trader Joe's or other natural/whole foods type stores.