When I was transferring this morning at Schipol, the staff directed non-EU citizens with Schengen area residence permits to the "EU" line at passport control. Is this always allowed for people with residence permits, or was it just because the lines had become particularly unbalanced?
No, it isn't generally allowed but it is indeed foreseen by the Schengen regulation when the queues are particularly unbalanced. When it does happen, whether third-country nationals (i.e. non-EU/EEA/Swiss) are allowed to use other lanes is up to the border guards.
The rules about this are defined in article 9 of the Schengen Borders code.
2. (a) Persons enjoying the right of free movement under Union law are entitled to use the lanes indicated by the sign in part A (‘EU, EEA, CH’) of Annex III. They may also use the lanes indicated by the sign in part B1 (‘visa not required’) and part B2 (‘all passports’) of Annex III.
Third-country nationals who are not obliged to possess a visa when crossing the external borders of the Member States in accordance with Regulation (EC) No 539/2001 and third-country nationals who hold a valid residence permit or long-stay visa may use the lanes indicated by the sign in part B1 (‘visa not required’) of Annex III to this Regulation. They may also use the lanes indicated by the sign in part B2 (‘all passports’) of Annex III to this Regulation.
(b) All other persons shall use the lanes indicated by the sign in part B2 (‘all passports’) of Annex III.
“Persons enjoying the right of free movement” means EU citizens but also members of their family travelling with them or joining them, even if they are not themselves EU citizens. Note that residence permit holders are also mentioned and can use the ‘visa not required’ lanes (because they do not, in fact, require a visa) but not the ‘EU, EEA, CH citizens’ lanes. Everybody may use the ‘all passports’ lane, all the time.
The same regulation also (kind of) provides for what you noticed:
- In the event of a temporary imbalance in traffic flows at a particular border crossing point, the rules relating to the use of the different lanes may be waived by the competent authorities for the time necessary to eliminate such imbalance.
(Without this, it would not legally be up to the border guards to ignore the rules, even temporarily.)
Why they would specifically invite residence permit holders to use the EU citizens lane is not clear to me. In principle, they should be subjected to the exact same ‘thorough’ check than visa holders, including the stamping of their travel documents, so why not allow everybody to switch lanes? The regulation does not provide for any distinction between residence permit holders and other third-country citizens.
Maybe Dutch border guards think residence permit holders are somehow easier to deal with or less likely to need secondary evaluation and be refused entry but it seems questionable from a legal standpoint (it's either follow the rules detailed above or waive them completely, there is no mention of any possibility to allow specific people to use the EU citizen lane).
The only exception to that principle are holders of residence permits as “family members of an EU citizen”, who are also generally people enjoying the right of free movement and therefore liable for a lighter check (with no stamps) than other residence permit holders and allowed to use the “EU/EEA/Swiss citizens” lane at all times.