One thing that can have an unbelievably strong effect is also wall proximity, both behind the amp and in front. Bass waves have such a long wavelength that they literally aren't audible in spaces smaller than the frequency demands. Also guitar amps, particularly open-backed Fenders etc. can sound drastically different when placed against a wall/in a corner; especially crunchy sounds can change totally. Battled with these issues a lot gigging in very small venues back in the day, both as a bassist and guitarist.
Dee
"When life's a biatch, be a horny dog"
Amps: Marshall JVM 410H w/ Plexi Cap mod, Choke Mod & Negative Feedback Removal mod, 4x12", Behringer GMX110, Amplitube 3/StealthPedal
Half a dozen custom built/bastardized guitars all with EMG's, mostly 85's, Ibanez Artwood acoustic & Yamaha SGR bass, Epiphone Prophecy SG, Vox Wah, Pitchblack tuner plus assorted pedals, rack gear etc. for home studio use.