Can agencies such as the NSA or GCHQ track what websites I'm visiting if I'm using the Tor Browser Bundle? What about hidden services?
Your question is quite hard to answer, because as far as I know the special capabilities of the agencies in this field are yet unknown.
However you can first look into Tor's design document. Section 3.1 states:
A global passive adversary is the most commonly assumed threat when analyzing theoretical anonymity designs. But like all practical low-latency systems, Tor does not protect against such a strong adversary.
So if you assume that the NSA, GCHQ or any other entity can observer world-wide traffic, Tor doesn't protect you here. Furthermore Matthew Edman and Paul Syverson found more weaknesses when an adversary has can look over many autonomous systems (AS). See AS-awareness in Tor path selection (PDF).
On the other side you can ask yourself why NSA or others will target your person. If they have a special 'interest' in your data, it might be easier for them to install some kind of malware onto your system or to break into your apartment and install a keylogger. Usually this can be done without anybody noticing it. It furthermore has the advantage for the adversary that they can be quite sure to get your traffic data. In the case above they need to apply algorithms which might also lead to wrong conclusions.
In addition to Jens' answer, from the front page of Tor project website:
For most uses, Tor provides the best available protection against a well-resourced observer. It's an open question how much protection Tor (or any other existing anonymous communications tool) provides against the NSA's large-scale Internet surveillance. On its own, Tor can't protect against attacks against vulnerabilities on your computer or its software; Tor is not the only tool you need to be secure on the internet. We're working on writing clear explanations for the issues, and the state of the research field as it stands. In the meantime, Bruce Schneier's advice may be useful.