Okay, I found at least 11 instances, probably more. Can't trust tagging to always be accurate. The fact that the tagging is as good as it is is impressive in itself. Within this, there are a few I am questionable about. There were more nose rubs when tied to sneezing, but I made to sure to NOT include any that were from sneezing. They all had to appear randomly. I did include a few due to sickness, but there were no sneezes within the particular comic. So no pre-sneeze or post-sneeze nose rubs included.
This first one surprised me. I don't know if I could this as a rubbing due to a tickling nose. She is holding back tears and sniffling, not really due to a tickle. But I included it to show you.

Another one that surprised me is here by Moondancer. She was trying to sleep but did rub her itchy nose. She is not a character we see tied to sneezing at all.

Now let's go through all the Twilight nose rubs I could find not tied to sneezing. These just occur naturally and randomly. It still makes me think she has a sneeze she is trying to rid of though.
Here is one of Twilight while drinking some alcohol. She admits in a later episode that being tipsy makes her nose tickle and she sneezes from it. This episode we see her rubbing her nose while a bit buzzed.

Here she either covers or rubs her nose when Pinenut pays her a visit. She had cat fur allergies.

I am not sure if this is a nose rub or an eye rub, but it does seem like her nose is being pushed to the side a bit. I do think this is an eye rub, but I wanted to include it just to show you. So I will not call this a nose rub. We see now "sniffing" text around her.

In this instance, Spike comes in covered in pollen and Twilight quickly goes to cover her nose. Not sure this is so much a nose rub as it is a defensive maneuver. So I won't count this one.

Let us check our nasally voiced Vinyl Scratch.
She seems to rub her nose fairly often, especially when playing games. I think it's because (made up theory alert) her nose is usually stuffed up.

Here she rubs her nose again likely due to a tickle and again while playing video games.

Now we move on to Starlight Glimmer, who is far more sniffly than I ever remembered.
While sitting on the couch, we see her here rubbing her nose and getting rid of that itchy itchy.

Starlight has a cold in this one but doesn't sneeze in this comic (nor any time we see her while she has this cold, ERRG!!) She admits to Gray she really needs to blow her nose and is seen here rubbing it because to probably tickles a lot. I really like this one.

Starlight is shown here again randomly rubbing her nose and sniffling as she does it. She must have a tickle.

So who do you think has the tickliest nose that needs the most rubs? If you know of others, please share them!