We noticed a skin-colored bump on Cooper's "upper lip" maybe 2-3 weeks ago. My husband assumed it was a doggie pimple and tried to squeeze it to see if there was any puss or fluid inside. He now thinks it may be more of a skin tag, as it does not appear to be filled. But last week we noticed a second and third skin-colored bump forming on either side of his "upper lip". The original bump is the biggest, you can see it clearly in the photo below. The second and third bumps are much smaller. They don't seem to bother him at all, even when my husband examines them. Might they be pimples? Warts? Skin tags? Something altogether different? Do you think they warrant a trip to the vet at this point, or should we wait to see how they progress on their own first? Thanks for your insight! (Sorry for the large pics, I wanted to make sure you could see the bumps.)

It might be  Canine Papillomavirus. How old is Cooper? Less than 2 years?

Here's one link. Query for lots of othters.
http://pet-diseases.suite101.com/article.cfm/canine-papilloma-virus

It is common around and in the mouth but the warts can appear in other places - between the toes, on chest and neck, etc. It (hopefully) will go away on its own. If the warts get big, they could get caught on stuff and cut or damaged. They may also start dying and then stink like crazy (rotten dog wart flesh)

The vets I showed it to didn't seem to have much knowledge or experience with it. I ended up knowing more than they did by researching on the internet.

Eventually the dog's immune system builds up and it goes away on its own. Fingers crossed.

One of my dogs had big, dangling warts. Literally looked like little cauliflowers on a thread.  I wondered what would happen if I just got a sharp pair of sissors and cut off the dangling part. I chickened out because I didn't know how much it would hurt my dog or if it would bleed a lot. I went to a vet I sometimes use. All he wanted to do was put the dog under and operate and cut the wart out by the root. This wart was one that was rotting. I'm glad I didn't have the vet do anything as the dog started to lick/chew on it and then all the warts started to go away shortly thereafter. No sign of them at all now. My dog was young, under 2.

Disclaimer - I have no human or animal medical training at all.

It's probably canine papilloma virus (puppy warts).  Koda had it when she was a few months old.  I think she got it from drinking out of the communal water bowls at Petco (won't let that happen again).  She had one on her lip that started off looking like an ingrown whisker, but kept getting bigger.  We ended up having it removed, which went fine, but a few weeks later she started getting them in her mouth.  The vet said that they will build up there immune system, and they would go away eventually.  I found FlexPet online, which is supposed to build up their immune system to get rid of the virus.  I didn't want to have to pay for another expensive surgery, so I tried it, and it worked.  Here's the link:  http://www.caninepapillomavirus.com/canine-papilloma-photos/

These two were some of the bigger ones. If you gently pulled on them, they just seemed to be attached by a thin bit of skin.
There were also smaller ones. There was one about the size of these on the neck where the collar was. That one started rotting and was really stinky.
Now they are all gone, can't even tell they were there. They probably lasted about 3 months. Started out small. Some didn't grow, others did grow. Some regrew after they were damaged.