Consider the 'Q' knob again (or 'Q factor', or 'bandwidth', or whatever they've called it on your plug-in), you might want to broaden the bandwidth slightly so that it is cutting a slightly larger range of frequencies.
Have a fiddle around with this parameter until you've found the sweet spot.
There might be more than one frequency you want to get rid of, so just repeat this process again.
Sometimes, you might have a clump of frequencies in a similar area of the spectrum, such as the low mids, which are giving your tone a certain undesirable characteristic.
Too much prominence in the low mids could make your tone sound 'boxy', or slightly wooden and dull. Consider cutting a number of pinpointed offending frequencies from the low mids, or even just setting a wide bandwidth and cutting a large chunk.
So far, all I've talked about is cutting, and not boosting. Well generally, it's not the best idea to use EQ plugins to boost certain frequencies, because then the digital plugin begins to flavour your tone and leaves its signature all over your sound.
It also means you might be clipping the signal in certain places and increasing white noise.
If you have a good plugin though, or even an analog EQ rack unit, then it's not the end of the world, and to be honest, I've boosted frequencies using some pretty cheap EQ plugins, and I've managed to get some great sounds.