There are quite a lot of Wizarding families who, I assume, live in places inaccessible/invisible to Muggles. However, there are examples of families who live among the Muggles, so their neighbors know about their existence, they just think they are a bit eccentric. However, if they openly live in a house on a Muggle street, it means that their address is registered, their house is known to the Muggle government, and they have to pay property taxes. They would probably also require some kind of Muggle ID documents.
Judging by the fact that said Muggle-meshing Wizard families aren't allowed to mind-control Muggles willy-nilly due to International Statute of Secrecy; AND would be carted off to jail if they avoided their taxes the same way Daywalking Vampires do; it stands to reason that the wizards who are known to Muggle world pay taxes because we never hear of Wizarding families going to jail.
Also, out of universe, JKR is very pro-taxation and anti-rich. So if anyone cheated on their taxes, it'd be the Evil Rich Malfoys and co... and we all know that Malfoys wouldn't be caught dead living in a Muggle world.
Well, if they're living among the muggles, in a house that is plainly visible and accounted for, then it would make sense that they would have to pay property taxes. Also they would probably be a target of investigation by HRMC or something like that, as they would have no official income, yet they would still somehow have money to lead comfortable life.
But more importantly, this leads to a bigger question: Should wizards pay income taxes? And if so to which government? Consider a business owner in Diagon Alley. He's definitely a UK resident, but he's not really a part of UK economy, nor he gains much benefit from services offered by UK government, for the taxes he would pay. On the other hand there is the Ministry of Magic, that also needs money to operate (if nothing else, it has to pay it's employees). I would guess that wizards pay taxes to MoM, which would make sense. Ministry could then take care of the muggle taxes, using a portion of taxes collected from the wizards.
Good solution would be to register all wizards who live among muggles as employees of one fictitious company. The Minister of Magic could then agree with the muggle Prime Minister on the portion of taxes wizarding population owes to the muggle government (considering how much they benefit from the public infrastructure), and pay it through the fictitious income of the fictitious company. "Muggle known" wizards would be covered as tax payers; and as there is probably not a whole lot of them, the fraction of wizard taxes used to cover them would not be large (there is more "secret" wizards, that still have to pay wizard taxes).
My guess is that they just wave a magic wand over a blank sheet of paper and mail it to the IRS. Or the British equivalent. It worked for Dumbledore in Book 6.
The Ministry of Magic probably pays a fixed or almost fixed sum in taxes to Republic of Ireland and UK government using a fake company stationed in the two countries. Probably one or two guys at Ministry of Magic who has taken muggle studies makes this happen. The sum would be small enough not to raise any suspicion (only about 5 k wizards at most on the British islands) and if it does the Ministry of Magic guys can use the confounds charm.
The Ministry of Magic then adds a reasonably sum to the income taxes the wizards pay to make up for the money the MoM pays on the wizards behalf. Wizards who live in muggle houses or own muggle stocks and bonds probably pays taxes on them just like a muggle.
There are no wizards who are prominent in the muggle world so wizards paying no income tax would not raise much suspicion since the only wizards known to muggle authorities are the very few who pay taxes on capital like real estate and stocks and bonds. If there is any suspicion they can just use the confundus charm or obliviate.
I could see a couple options, depending on the interaction with the person or family in questions. We know that Wizards tend to squeeze their urban centers in between existing centers (platform 9 3/4, the The Blacks' residence in Order of the Phoenix in a town home in between other homes), so those may or may not "exist" on the books of Muggle census and real estate information. Are we looking at a Perception Filter/Someone-Elses-Problem field, where it actually exists but no one cares? Or are they literally creating space where there was not some? That is a question that is never really answered, other then the larger-on-inside aspects of Hermione's bag or the pup tent that shows up every so often in book 4 onward.
The only other option we see is in the Lovegoods, Weasleys & Malfoys, that have family estates of various sizes in what seems to be the middle of nowhere. They could be listed and owned privated estates, where the owners simply pay property taxes, or they could simply be in public land and fall into the Perception Filter category.
Assumably those that have some interaction with the Muggle world would pay taxes. But with the European wizards consisting a veil of secrecy and illusion for everyone other than the Prime Minister, we won't know unless there's supplemental information (as opposed to American Wizards, which are in the Yellow Pages under "Wizard")
Non-muggles may well have paid muggle taxes, but then this might've been refunded to them, depending on their usage of muggle public services. After all the muggle government was both aware of, and had formal relations with the ministry of magic didn't they?
So what someone would've paid in pounds, they'd have got as tax refunds in sickles and galleons.