Dave, you can improve your sounds even more by not sticking to a fixed 40Hz low pass filter, but moving it up to the bottom of the audio range of the signal, especially on miked recordings but even on pre-recorded samples. E.g. A lot of vocals really have nothing much below 200Hz, (obviously some low male voices will have stuff down to about 100Hz so you need to listen and move the frequency point to where there's no audible difference) whilst there can be a lot of extra noise picked up below that which can muddy the mix and also falsely trigger compressors. Do it on several tracks and it is amazing how much clearer your mix can be. You can also employ a low pass filter on the higher frequency sounds to help reduce extra noise.

It's also often useful to use an EQ that has adjustable HP and LP filter slopes. Often the built-in ones have a mild 12dB/octave roll-off, which can still leave audible noise below/above the cut-off point. Something like the Tokyo Dawn Labs free TDR Nova dynamic EQ http://www.tokyodawn.net/tdr-nova/ will give you the options of much steeper slopes. The paid-for Gentleman's Edition version (which I use a lot) goes even steeper. This can be really useful on some problem tracks with a lot of bleed from other instruments.

Also, don't forget that at the indicated filter cut-off point, the signal is already 3dB down, so for bass guitar (low E fundamental at 42Hz), with a high pass filter at 40Hz you are reducing that fundamental slightly. So you've either got to set the cut-off point lower at say 35Hz, or use a filter at 40Hz with a much steeper slope so that the affected area above the filter cut-off point is much smaller.

Bottom E on a normally tuned guitar is at 82Hz, so you can set a filter at say 75Hz to cut off all extraneous noise below the guitar. Especially with gentler filter slopes, the higher up you can put the filter, the quieter any sub-sonic noises will be. E.g. with a 12 dB/octave slope set at 40Hz, any noise at 20Hz will be reduced by 15dB (because the filter is already at -3dB at 40Hz). But if you can set the filter at 80 Hz (an octave above 40Hz) then any noise at 20Hz will now be reduced by another 12dB, so will be 27dB quieter.

Or you can have the same effect by using a 24dB/octave filter set at 40Hz, which if then set to 80Hz, will reduce any 20Hz noise by 51dB, making it pretty much negligible.

So I tend to use this EQ as the first insert on most of my tracks (let alone using its other EQ and dynamic functions).