I use peauction only when i can't login in game, but ingame auction markups are the best way to know rpcies exactly, since external websistes give a lower markup price because they don't count buyouts.
I think there was quite a lot of controversy about these various sites and a lot of allegations of market rigging etc. I will usually consult peauction when in doubt about a special item, because they seem to have a more advanced algorithm, with smoothing etc. For quick price checks the ingame stats are usually good enough. The moral is; who do you trust?