Let's start with some magical history. In Dumbledore's notes on The Wizard and the Hopping Pot (one of the Tales of Beedle the Bard), we learn about Muggle-Magic relations prior to the International Statute of Secrecy:
By the seventeenth century, any witch or wizard who chose to fraternise with Muggles became suspect, even an outcast in his or her own community. […] “Let the Muggles manage without us!” was the cry, as the wizards drew further and further apart from their non-magical brethren, culminating with the institution of the International Statute of Wizarding Secrecy in 1689, when wizardkind voluntarily went underground.
I think we can reasonably assume that (at least in the UK), since the Gregorian standard was in place by 1689, the magical community were using it when they separated from Muggles. We know from scenes at Hogwarts that the magical community celebrates (or at least recognises) Easter, which is a key feature of the Gregorian calendar, so I think this is a plausible candidate.
The Gregorian calendar is still in modern use in Western culture, so I'd expect the magical community to still have it, as well. I can't think of a good reason for them to switch, other than magical arrogance and a belief that anything used by Muggles is tainted and wrong. (And I doubt that would convince anyone.)
For other countries, it's harder to say. We know that the magical community is global, but there's never enough detail given about them to decide whether they're using the same calendar as their Muggle counterparts.
I know that Harry Potter Wikia isn’t usually considered canon, but they have a list of dating contradictions which looks fairly accurate. To me, most of this list can be written off as JK Rowling's dodgy maths, but I thought I'd pick on one example.
For example, in Goblet of Fire, we have Friday the 30th of October and Tuesday the 22nd of November. If you look at a calendar, you see that 22 Nov falls 23 days after 30 Oct, so the 22nd is a Sunday in the Gregorian calendar. There are many possibilities:
- Whoops, JK Rowling messed up.
- Their weekdays occur in a different order to ours.
- The magical calendar puts extra days at the end of October.
- There are some "glue" days between months to make up the difference.
- Unclear as to whether to start months from the 0th or the 1st day, they compromised and count November from the (-1)st.
- At some point, several days were dropped,1 but nobody thought this was remarkable or unusual.
I think the only plausible explanation is (1).
As for the case of the Nimbus 2000:
We know from the answers to/comments on that question that the Nimbus numbering scheme isn't set up to reflect the year in which the model was released. And since they've only released four or five brooms in forty years of business, the N2001 will probably still be current in the actual year. This system seems "futuristic", rather than pinning it to a year and highlighting how long it's been since your last update.
In Chamber of Secrets, we learn that Nearly Headless Nick died in 1492, and they're celebrating his Five Hundredth Deathday Party, so CoS must take places in 1992. This rules out the possibility of a shift (e.g. Muggle 1992 is wizard 2002) unless they've dropped even more time than we thought.
1 Actually, this can happen in real life. Calendars are really weird. Sometimes 75 seconds shows up out of nowhere, or you'll suddenly jump forward ten days. With the ten days you jump depending on your country. And their religion. It's one of the efw ways in which real life is stranger than Welcome to Night Vale.