I always send self-sealing envelopes. I'm sure the agencies appreciate having them to send my rejections.
YES WE DO. Every time I see that self-sealing flap, my mind cries a little "Yes!" We certainly don't hold it against authors if they use traditional envelopes, but yes, I am licking them. And yes, I have diseases, and no, Herpes Simplex I is not an STD, it's something you get if you have a lowered immune system because you're on an immuno-suppressant (Damn you 6-MP!), stop looking at my cold sore, it's not what you think!
...But I digress. Germs and bacteria die when the envelope dries. I think you would have to eat the envelope within an hour of my licking it to actually pick up my cold, and to my knowledge, people are not in the habit of eating envelopes as much as just throwing them in the trash.
What we really despise is people who enclose an SASE from some stationary package, where the envelope is too small to fit the return letter unless we fold it up a million times. Don't do that.