Solution 1:

You definitely want to use a for-each loop to enumerate each user and apply the license. The loop needs to call up the .UserPrincipalName from each object returned in your Get-ADUser query, as Office365 needs to work with that value when setting licenses:

Get-ADUser | %{ Set-MSOLUserLicense -UserPrincipalName $_.UserPrincipalName }

I have created my own answer here to explain a common case that I think you're describing in your question: You don't want to blanket apply the same license options to everyone.

A TechNet Blog on this matter is immensely helpful. You may not want to give your Finance team access to SharePoint Online/OneDrive for Business for data leakage reasons, or you may have a call center who you don't want to enable for Lync/Skype for Business.

To get information on your tenant, start at the top:

Get-MSOLAccountSku

This will return the license packs you have in your tenant. Some common SKUs are ENTERPRISEPACK and DESKLESSPACK. These will be listed by yourorg:LICENSEPACK under AccountSkuId.

It is important to note that each of these License packs can have features disabled from them when you apply via PowerShell (similarly, you can choose to check/uncheck option boxes in the Admin Center).

LicenseOptions

To create this subset of license options, create a new variable and leverage the New-MSOLLicenseOptions cmdlet: $LicOpt = New-MsolLicenseOptions -AccountSkuId "yourorg:ENTERPRISEPACK" -DisabledPlans OFFICESUBSCRIPTION,MCOSTANDARD,SHAREPOINTWAC,SHAREPOINTENTERPRISE,RMS_S_ENTERPRISE

(The above options would correspond to the screenshot above, I'm sure you could guess that I totally pulled it from a provisioning script.)

Finally, we can tie this back to your Set-MsolUserLicense in your ForEach loop:

$LicOpt = New-MsolLicenseOptions -AccountSkuId "yourorg:ENTERPRISEPACK" -DisabledPlans OFFICESUBSCRIPTION,MCOSTANDARD,SHAREPOINTWAC,SHAREPOINTENTERPRISE,RMS_S_ENTERPRISE

Get-ADUser | %{ Set-MsolUserLicense -UserPrincipalName $_.UserPrincipalName -AddLicenses "yourorg:ENTERPRISEPACK" -LicenseOptions $LicOpt }

As always, your tenant may vary. I hope I've given enough info for you to discover the options available and apply appropriately!