I think it's difficult to say whether there is the best assay for assessing oxidative stress.
There is an assay for total oxidant or antioxidant activity of a biological specimen. However if we do the assay, we don't know the contribution of antioxidant species involved. MDA or TBARS assay is very sensitive, yet not specific, carbonyl is a measure for oxidized protein and probably not specific for fat or carbohydrate. So, I think I would do a series of assays like mentioned by others in this communication, e.g. MDA, F-isoprostane plus SOD, GPx or catalase. Depending on the subject you want to study, may you need to do DNA adduct assay too.
malondialdehyde (MDA), protein carbonyl (PCO), reduced glutathione (GSH) levels, and the activities of glutathione S- transferase (GST) glutathione peroxidase (GPx) could be of immense help in determining oxidative stress status in rodent tissues.