In terms of commercial tools or open-source ones, I think Ketchup's statement
This doesn't happen as much any more, but in litigation, tools used to always get questioned in terms of repeatability and procedure. Guidance has a team of attorneys that are ready to hop on a plane and testify in court on the solidity of EnCase.
is quite true. Open-source tools offer traceability and transparency, though the sourcecode must be read by someone, otherwise it doesn't matter if they are OS or not. In court often offensive questions are asked and reliability must be proven. Additionally the investigator should be able to reproduce the results with different tools.
Whichever tools the investigator is going to use, several questions should be answered (limitations, function volume, automatization, approved by other experts, etc.) before going on. Also it might be better to use tools from the same architecture as the target system is.