Derral's already made and pulled up some good examples of where 3rd party lens makers can make lenses that are simply not sold by Canon nor Nikon and also have a very high quality to them. In addition to that there are some examples where the 3rd party lens can also beat out a lens by Canon and Nikon - the Sigma 50mm f1.4 is a prime (yes pun intended

) example of a lens which is capable of optically beating the current canon brand option (not as sure about the nikon).
I've also seen impressive results comparing a canon 500mm f4 against sigmas 300-800mm lens at the 500mm mark where the sigma was standing on par image quality wise - not what you'd expect from a lens with a long zoom throw.
In short the best advice is to:
1) Decide what use/limitation you have with your setup that needs resolution via adding new glass - ie have a clear and defined use for the item - criteria.
2) Work out a budget - might be totally ballpark at this stage, but it gets you somewhere to start from.
3) Look at the market and consider all the options - own brand and 3rd part and see which ones fit into your budget; but also look at what lies below and above. Sometimes you might find something cheaper that is more ideal and other times you might find something that, with a little more waiting and saving, gives you a significant advantage.
If I had no budget limits and remained with 1.6 crop you'd probably see me buy most of the setup I own now - which has 2 canon, 3 sigma and 1 tokina lens in it at present. Though with the added budget there'd be a few more canon added to the list, but not to replace the 3rd party options that I currently own (possible exception on the 35mm, but its not a major pressure point for me that focal range so I'd probably save the money and keep the tokina).
For reference : Canon 70-200mm f2.8 IS L MII; Canon MPE 65mm macro; Sigma 150mm f2.8 macro (someone please buy the darn thing from me so I can get the OS edition!

); Sigma 70mm f2.8 macro; Sigma 8-16mm; Tokina 35mm f2.8 macro