I think the main difference is the licensing model.
Authenticated sites costs are based on monthly logins (same customer logging on 10x/day is bad). We use this one because you can have a LOT of infrequent users.
The customer portal licenses are based on user count.
There are some sharing rules and object access differences, too. One sucky example on auth sites is that users can't update their account directly without a custom page plus wrapper class.
Definitely tell your account rep what you're trying to do and think about what scaling would look like...that is, how to scale customers without scaling costs.
Great question.
First, watch this video: Ready to Partner with Salesforce.com (ISVforce or OEM)? (http://www.youtube.com/watch?v=_oV9LthQ5O0)
ISV companies can sell licenses to their own apps (which I would say is the most common - this would be using the AppExchange to sell, say, 5 licenses of a managed package app. With new AppExchange checkout features from Stripe (formerly from Recurly) you can charge easily for those.
Some companies want to make money on selling CRM licenses while offering customers a discount on their CRM licenses. These are custom licenses (ISV) that are contractually limited to certain objects and permissions. There is a lot of trust here, and salesforce.com can verify at any time that the end-customer is using only objects that are allowed.
As far as charging for those, the ISV charges "twice" for the product - one fee per app-license and one fee per CRM-license... but generally this is presented to the customer as one charge.
The customer can use this ISV app as part of a larger org, and can sign up for this app using Trialforce, an AppExchange free trial, an AppExchange install with a trial period expiration date, and more. This is for an app that will fit into a larger business process.
That's pretty much the ISV side of it.
For OEM:
OEM and Embedded are the same thing (in case that comes up)
OEM licenses are for the internal app. For portals, consider ISV Portal licenses (yes, the naming becomes confusing). Of note, ISV Portal licenses don't have Chatter enabled and are required to interact via a Force.com site. Think of them as Authenticated Website or Customer Portal licenses. (http://www.salesforce.com/us/developer/docs/packagingGuide/Content/oem_user_license_comparison.htm)
OEM allows someone to use Salesforce as a controlled container for presenting an app. I'm working on an app right now, and have decided on the OEM model because I want the end-users to be able to do zero customization. I will have one admin user who will see that it is Salesforce, but all other users will interact with the app via a custom interface built in a Force.com Site.
Here is my big concern, and the place where I'm trying to do more research: Chatter Plus licenses are $15 per month (for just CRM). I'm trying to find out how much salesforce.com will charge me for the OEM licenses. I'm hoping that I will be charged less than $15 per user per month for each OEM license. And, of course, I need to add my own fee on top of that.
So to answer your question directly: OEM licenses allow the customer to assign a user to my app. Whereas an ISV app will allow me to add more custom fields to objects included in that app, an OEM user cannot see any fields other than those listed in my application. ONLY things in my namespace are available.
Another outstanding item on my list is to ask: What can the full Salesforce System Administrator of the org I'm giving my customer do? Every org requires at least one full user, and I'm waiting to hear back on what permissions that user has. It's probably irrelevant, as that person can't add more licenses to the org, and no users can see any customization the admin does, but it's worth looking into.
So a more direct answer: ISV app licenses are "bigger" than OEM licenses. An OEM agreement may sit as part of an ISV agreement. OEM licenses are not something commonly sold on the AppExchange. The AppExchange is for plugins to extend Salesforce. OEM apps are intended to be the complete representation of the app - that happens to use Salesforce as its platform, so the users may not even know they're using Salesforce if it is configured that way.
I hope this helps.
Best Answer
You won't be billed beyond the available licences, you're just billed for the licences you have. That said, you may not be using all of your licences if you have deactivated some users and not added new users.
To reduce your licence count your administrator must file a case with support, using "Licence Reduction" as the subject line as shown in this knowledge article.
So yes you do have to manually reduce licences by filing a case. As for features I'd expect those to work in the exact same way.