I like tweaking new bikes to suit my tastes and here's what I do:

1. new saddle
2. new rims--Mavic Crossmax SLR for the mtb, Ksyrium SL for the roadie
3. new cranks--FSA with sealed ceramic bearings

I'm also debating about putting on a different cassette on the roadie and a Salsa mtb handlebar for the Epic.