Please advise from your point of view when the benefit of a unified installation using multisite outweighs potential problems with plugins.

We plan to have around 6 sites, we do not have any hosting related limitations (own server). We plan to have more Joomla installations with ldap integration (mostly same users in the various instances) and different content but almost the same extensions, plugins and
components. Templates will be different on every installation.

Is it recommended to use the multisites extension to manage this instances or is it better to have standalone installations to avoid problems with different extensions and their updates?

One advantage of JMS is the maintenance when there are update or bug fix distribtuted for some extension or plugin.

If you have 6 standalone website, this also mean that you have to maintain 6 Joomla and also 6 times the extensions installed on the website.

When you use JMS, you can benefit on the fact that the files and folder on the disk are shared between the websites.
For example, you will just have to update Joomla 1.5.9 to 1.5.10 only once as this is the same files for all the website.
This is also true for the extension when they does not impact the DB layout.

At the origin, I have create JMS to reduce the maintenance.
Imagine that you have 100 websites and that you need 30 minutes to install 1 joomla, this mean that you will need 3000 Minutes (50 hours) to just install Joomla.

With JMS, you can do that faster as you have only 1 joomla installed. You just have to create and fill the DB.

I have customers that manage several hundred of websites (> 200). I have a customer that has more that 1000 (1 thousand) websites.

See User Manual chapter 8 for different maintenance scenario.

For your information, I am currently working on the user sharing and perhaps (???) I will have a solution in june or july.

This is similar to my present consideration. I'm a potential customer so any advice is gratefully received!

I have a site with it's own domain and beneath this there are some 'sub' sites.
The way this is set up is that each 'sub' site simply has a Joomla page link to a 'home page' beneath the main domain. The only thing differentiating the 'sites' are sections/categories, templates and menu configurations.

I guess I could use SEF and the sec/cat URL would look tidier at least, but it doesn't stay my doubt that it would be much better to give each 'sub' site it's own domain.

I'd rather set something up now that have a much bigger headache down the road as these 'sub' sites proliferate.

There is very little difference between each 'sub' site, or even between them and the main site for that matter apart from some simple aspects of the template/page naming/content and I'd very much like to keep the entire project in one folder. The icing on the cake would be synchronised admin for all the sites, but hey!

Thank you for reading this far, best wishes.

With JMS, you can have this structure of main site and sub-dite.
With JMS, you can simplify the maintenance of Joomla as you will have only one.
This will reduce the disk space, the update of the PHP code, ...

You can effectivelly have different domain name for the sub-site.
With Multi Sites Menu Type component, it is also easier to define your menu between the websites as it is possible to benefit of JMS to directly use the correct redirection.
This can reduce the maintenance when you change the menu in a sub-site.

Concerning the User Sharing, I am currently working on JMS 1.2.x that will solve this problem when working with several websites.
I already have a prototype working.
I hope this new JMS version 1.2.x will be available in june or july.

The User Sharing will really share ALL the users between the websites.
All the users will be saved in one and only one websites.
All the other websites will share the My DB users tables.
This will require MySQL 5.1 version. I still have to check the release version. Perhaps MySQL 5.1.2 or higher