ויד המגיה תיקצץ

One of the things that distinguishes Yeshiva learning from ahem "mechkar" is their seemingly different approaches toward establishing an accurate girsa in the Gemara. I think Yeshivas are generally reluctant to do this because first of all, the printing of the Vilna Shas "canonized" the text of the Gemara, to the extent that anything appearing in parenthesis will be skipped without being read, while anything in brackets will be read in automatically. To a certain extent, this is understandable because Yeshivas are not (and should not) be studying the Gemara, but what the Gemara says. Another reason for this is that this is just way out of their league. In order to establish a girsa, you need to compare editions that may be impossible to get, you need to learn the different layers of language, etc. etc. and besides for the fact that this is time comsuming, it also is not very engaging to the vast majority of yeshivaleit out there. It doesn't make them feel smart.
So the job was left to the Vilna Gaon, the Bach, the Messores Hashas, and the dude who puts in "Chilufei Girsaos" in the Wagschal Shas. The truth is, though, that all of these leave something to be desired. Yeshiva legend has it that the Vilna Gaon did not change a girsa uness he had 150 proofs that it was off. I remember having a problem with the reading of a braisa quoted in the Gemara. So I did what any good yeshiva boy would do: I looked at the margin and saw that it was Tosefta X:Y. Flipping there, I saw that the only way the Gemara's braisa was found in the Tosefta is if you stuff about three lines in to make it identical ---which the GRA did. Even then, the Tosefta didn't match exactly (for one thing, it didn't include the problematic words, which actually was the part the Gemara needed most for its discussion.) Somewhat disappointed (and i still don't understand the Gemara) I came to the conclusion that the Gemara was quoting a different braisa, and the GRA must have changed the girsa of the Tosefta to fit.
The Messores HaShas has a different feature, which is that I believe he changes girsaos to fit in with the Yeshivishe rules. For example, there is a rule that תניא is a braisa while תנן is a mishna. However, the rule only applies because of the many, many times that the Messores HaShas edited tanya and tnan to fit. If the change would only be made every once in a while, I'd be willing to accept it; however, the Messores HaShas makes this particular emendation so often that I'm willing to bet that the rule came first, and the fact was changed to fit it.
The Vagshal Magiah is almost not worth discussing, because he brings down differences in the text that are so minor that I'm tempted to ask "So what?" most of the time. (eg, changing גוי to עכו"ם and גזירה to שמד.)
The upshot? I think everyone needs to take any emendation with a grain of salt. To quote a line I heard somewhere:
"If the Gemara makes more sense without the Bach, don't use the Bach."