Hi Addy. I find that getting the kick to sit nicely in terms of pitch can be very difficult. Like Danny said increasing or decreasing pitch on kicks can really affect its sound. Even with something like Logic's Ultrabeat where u can transpose the sample up or down this can be a problem and sometimes more trouble than its worth.
In my own tracks I never usually make the key of the kick match with the bassline. However I tried this about a month ago with a tech house track that starts with just the kick and bassline, so I wanted them both to sound really coherent from the start. Anyway, I tried it for a while and in the end found that the root note (key) of the bass was just too low to transpose the kick to, it took all the punch and weight out of it.
However if you can get your tracks so the drums and bass are in tune with each other without too much bother then in the end it really gels the track together, it adds a very subtle coherency that you cant quite put your finger on (because pitch of drums are a subtle thing that not too many pay attention too afterall!)
http://www.youtube.com/watch?v=y5nlUtl8Ge0A good example of how drums/ bass roughly in key on a track can make it sound really tight.