Yeah, very often the sounds that your ears construe as a good sound (when recording seperate instruments) is your problem, cos you're hearing (for example) an electric guitar which you want to sound "full" or "warm" in isolation, but then if you put that in a busy mix it's that fullness that is the problem. When people here the finished song, they aren't going to be listening to each instrument in isolation, so you need to change the way you think about those instruments when you're tracking, and think where each instrument needs to sit in the mix.
What frequencies are vital to the listener, for them to recognise what what instrument is? There's no point trying to get some nice warm lower-mids and bottom end on guitar a lot of the time (unless it's JUST guitar and vocals), cos then you're not gonna be able to seperate it from the bass guitar or bass drum without some serious EQing later on.
As has already been pointed out, cutting lower mid on instruments is a great way of clearing things up in that region, but as others have also pointed out, bearing the finished product in mind whilst tracking will help more.
I was recording overdubs on a song last night, including sax, tambourines/shakers, handclaps, backing vocals etc, and when I was listening to the vocals (to set levels) they sounded a bit harsh and bass-light, but once recorded they fitted in the mix perfectly without needing EQ, and without getting in the way of anything else.
I was using a 421, which is great for that kind of thing.
If you want to hear that song as an example, or to slag off my song/playing/work, then either is fine with me, hehe:
http://laprecords.co.uk/studio/mp3s/ap_rebel.mp3I haven't done the final mix yet, but it's getting there.