There are several possible ways to answer this.
Play Statistics
One is tracking how often skills are being used in a campaign, and tallying that up. Thankfully, someone did exactly that and tallied up all skill checks for two campaigns of Critical Role that used the D&D 5e rules.
I wanted to have some concrete data on the most used skills in the game. There are discussions about this online, as well as ample anecdotal evidence--but I wanted quantifiable data. [...] Granted, Mercer’s table will not look exactly like ours but with 10K rolls to average out, the numbers might look pretty similar to what we experience at our own tables.
Here are the overall results, by skill:
| Skill |
# Rolled |
% of Total Rolls |
| Perception |
2,976 |
28.6% |
| Stealth |
2,141 |
20.6% |
| Investigation |
1,296 |
12.5% |
| Athletics |
656 |
6.3% |
| Insight |
543 |
5.2% |
| Persuasion |
517 |
5.0% |
| Acrobatics |
374 |
3.6% |
| Deception |
366 |
3.5% |
| Arcana |
257 |
2.5% |
| Survival |
201 |
1.9% |
| History |
196 |
1.9% |
| Nature |
193 |
1.9% |
| Religion |
169 |
1.6% |
| Intimidation |
141 |
1.4% |
| Sleight of Hand |
133 |
1.3% |
| Medicine |
102 |
1.0% |
| Animal Handling |
71 |
0.7% |
| Performance |
66 |
0.6% |
| Total |
10,398 |
100.0% |
Perception is by far the most often used skill, with more than a quarter of all rolls. Stealth comes in second, with a fifth of all rolls. 5e introduced Investigation as an alternative way to find secret doors and such, taking some of the load of Perception, and it comes third (if you used Perception for those Investigation checks, it would make up over 40%, so it makes sense to use Investigation whenever you can as a DM, to balance things). This is followed by Athletics, then the top 2 social skills, Insight (the social version of Perception), and Persuasion, and Acrobatics.
At the tail end, we have Performance at the least-used skill, followed by Animal Handling and then Medicine.
Why do we see such a big difference between Perception vs Performance? Perception helps you avoid deadly ambushes and traps, helps you find hidden treasures, helps you learn more about your environment to make decisions, and in the form of passive perception is always on. Performance needs to be actively initiated, and there are not that many situations where it helps or even can be used, and even if it can, successfully entertaining a crowd at the inn normally has much less severe consequences than spotting the ambush or not.
Likewise, animal handling may be of use early on, but as monsters get more dangerous, pack animals quickly tend to become a liability dying from a single attack, and beasts mostly are of lower CRs and cease to be opponents that challenge the party. Most of what medicine does beyond diagnosing is taken care of by spells like healing word, or even a simple healer's kit, and how important are diseases when you can just cure them with laying on hands or lesser restoration?
Modules
Another way to look at this is to see what skill checks are asked for by modules. For example, here is the tally from Lost Mine of Phandelver
| Skill |
LMoP |
% of Total Rolls |
| Perception |
19 |
39.6% |
| Athletics |
6 |
12.5% |
| History |
4 |
8.3% |
| Investigation |
3 |
6.3% |
| Persuasion |
3 |
6.3% |
| Deception |
3 |
6.3% |
| Arcana |
2 |
4.2% |
| Survival |
2 |
4.2% |
| Stealth |
1 |
2.1% |
| Insight |
1 |
2.1% |
| Acrobatics |
1 |
2.1% |
| Religion |
1 |
2.1% |
| Intimidation |
1 |
2.1% |
| Animal Handling |
1 |
2.1% |
| Nature |
|
0.0% |
| Sleight of Hand |
|
0.0% |
| Medicine |
|
0.0% |
| Performance |
|
0.0% |
| Total |
48 |
100.0% |
Granted, this is a much smaller sample size but again Perception takes the top spot (with nearly 40% of the total!), followed by Athletics, a high count of history checks, and Investigation. There is a somewhat heavier emphasis on social checks (Persuasion and Deception). At the tail end we again see Performance and Medicine; Animal Handling gets one mention, and it makes sense that it is a bit more useful in the first four levels that the adventure plays.