For me..

1) St George Budapest 1971-74
They won everything from GFs to winning the Interstate Championship beating all 4 Melbourne teams, to winning International Tournament in Japan beating the hosts as well as a leading Danish team Frem 3-0
To having half the Socceroos in a successful FIFA World Cup Qualifying campaign through Asia that includes Israel and NZ.
Special memories 

2. Brisbane Roar 2010-12
2 GF wins in front of over 50,000 fans including  one of which was the greatest GF ever played.
36 game unbeaten run
Thomas Broich…
Super Quality

3. Melbourne Victory 2006-07

A joy to watch Fred, Thompson with 15 goals
Averaged 30,000 per game
Won the GF 6-0 in front of 55,000…with Fred providing 5 assists for Archie
A super team…

I’d throw in Oceania’s team of the century as well 

A special mention to Melbourne City 2020-22.
A number of Socceroos and playing brilliant football

Wanderers under Popovic winning the ACL

Agree, I forgot about WSW but their first 3 seasons were massive.
Any suggestions for No 2 and No 3

Nah. Think you nailed it 

The Sydney side from 2016-18 is definitely better than the Victory side from 06-07.

Victory lost 4 games that season which was only 21 games long. Sydney lost 4 games over two seasons which were 27 games long.

Good point, so who is your 1, 2 & 3

I'll post my (unupdated) comment from the Australian Club Rankings thread 4 years ago when we were asked to estimate highest Aussie ELO rankings:

"If it was A-League only, it would be a toss up between Sydney FC at the state of this year and Brisbane in 2011-12. Victory towards the end of 09/10 season having come second after winning the year before would be pretty high as well.

• Sydney City are consistently top or near top of the league from 77-85ish and also won a couple of those weird non-counting finals - so they would have to be high. But at the same time  never run away with it and had massive streaks/leads like SFC/Roar did, so it's hard to imagine they got higher. I guess it depends on how short/long-term the formula is (i.e. does winning the league regularly over 5 years but never running away with it trump 2 years where you were untouchable? My guess is it doesn't).
• Marconi in 89-90 but will be pulled down by a poor league showing in 88 (despite winning the finals).
• Knights in the early 90s would have to be high. Towards the end of 92-93 and 95-6 they would have been quite high. The horror 93-4 campaign would have prevented them from having the all time high though.
• South Melbourne at the end of 98-99 and Wolves after 00-01 would both be high as well with both having won the final 2 years in a row (and finishing top 2 on the ladder each time). However again, they never ran away with the comp like we've seen in the A-League era. 
• Perth Glory obviously at the end of the NSL era. They topped the ladder with very few losses. They are my wild card for potentially topping SFC/Roar.

So my guess...?
1. Syd 
2. Roar
3. Glory (NSL)
4. Syd City
5. Victory
6. Marconi 
7. Knights
8. SMFC
9. Wolves"

A brilliant summary.

Looking from a different perspective.

well done 

I think a team under all the radars was the Arnolds CCM team culminating in the AFC game, the Championship winning team of 2012-13 played 2 days after winning the Grand Final.
By far the strongest defensive pairing to have ever graced the league in Sainsbury and Zwaanzwijk (plus Wilko in the first 2 years). 3 consecutive +50 results when the league was at its strongest. The only team to beat Ange in a finals games (2012-13 Semi CCM1 - MV0).
I know it may seem controversial but I don't see how you can mention Brisbane or WS, without dropping in that CCM team.

The other 2 I'd put as St George Budapest and Brisbane Roar..

A question were does WSW ( in its first 3 years and it’s ACL success) fit in

Victory's 6-0 GF win was by courtesy of Mathew Breeze...

What is your 1, 2 & 3….

Rate the 3 Best Clubs ever eh ?
Well is it personal pref or actual facts fugures - let face it titles are the facts right.
Therefore combined titles currently its :
1 SMH
2 SFC
3 Hakoah
OK its wiki but it does give a great brief on overall status of successful Clubs past to present.
https://en.wikipedia.org/wiki/List_of_soccer_clubs_in_Australia_by_competitive_honours_won

Some mentioned by some are way down the titles ladder.

And this doesn't even include the 10 State league titles :) 
I think the intention is to rate specific club season mate, not overall performance.... for arguments sake, 2022 South only dropped 16 points all year -- lead tabkle for 24 rounds, 14 (I think) clean sheets...... +39 goal difference.... that sort of thing.

Funny looking at the WSW honours.  Never A-League champions, and half of their honours come by way of being AFC champions once.

That’s interesting- can you put the years behind the clubs..

Johns you could spend the time in that link and get the year playing with the ascending tab I expect but TBH I couldn't be bothered spending the time for all that matters to me and anyone who looks up any leagues stats for what Club is most successful is by Trophies hauled nothing more or less.
Stating how a Clubs season was so sensational for eg like BR's epic undefeated run doesn't mean they rank in one of the best for me as good as it was.
So all have missed or preferred to not even mention SFC due to dislike yet they have the runs on the board got figure.
How do we rate Leicester's surprising EPL win - a brilliant feat but they rank 20th with another 4Clubs with 1 title for eg....

So I suspect your thread really is about who do you rate as your Top3 fav winning Clubs in Aussie football history.
By the way I agree STG back then were amazing pre NSL that was established in '77.
STG's success, nothing to be sniffed at but you've quoted this before.

Honours
Australian Champions                  1983
NSL Playoff winners                      1982, 1987
NSW Champions                           1962, 1972, 1976
NSW Grand Final Winners            1967, 1971, 1974, 1975, 1981
NSW Super League Champions    2013
NSW Super League Grand Final    Winners    2013
Ampol Cup (Preseason) Winners        1960, 1967, 1972, 1975, 1982

NSW NPL 2 Champions       2018

Not having a go at SM, but do you know the history of that award? It it's the IFFHS It was basically a few stats blokes in a bedroom who had some offical sounding body. 

Having said that SM, obviously one of the best clubs over history 

Does Bohemians Praha 1905 count as Aussie? 

The only fair way to measure it is through NATIONAL titles and cups.( 1977-2022 )
You really can't use state titles in your argument / viewpoint. IMO of course.

Tongue was firmly in cheek for that one.... :)

Hahahaha yeah its laughable ..... but somehow having "Oceania Club of the Century" on our crest REALLY pisses people off :) hahahahahahah

SMFC not really an "Aussie" club either though mate ...... are we?

:D

Agree but at the end of 1972 a interstate championship was held with the top 4 from Sydney meeting the top 4 from Melbourne at the end of the season. 

In 1976 St George and South Melbourne played a Home and Away unofficial champions of Australia.
South won both matches by a score of 2-1 for a 4-2agg

It was 1-1 in Sydney and then 1-2 to South Melbourne.
St George had lost just 1 game in winning the NSW 1st Division.
South Melbourne had lost 2 in winning the Victorian 1st Division.
So this was the Australian club championship playoff.
Interesting both clubs then struggled in the following years NSL…