It depends on the surrounding colors and how much you want to disrupt your users' attention. Red is generally associated with high level of alertness or "critical" warnings. However, it's used on many sites for neutral notifications because of the high contrast with the color of surrounding elements (many colors on SE, blue on Facebook, shades of gray on Google, dark green on Forrst, etc). This ensures high engagement with notifications but, at the same time, it may break users' interaction flow with your app since stark contrast draws a lot of attention.
Thus, if you want your users to act on notifications ASAP make them red (unless the surrounding elements are of reddish colors). Otherwise, blue will work, too.