Note: These are my summaries of the 1995 version of the guide, not the policies themselves.
Separation of Church and State
Policy 80 — Bus Transportation, Textbooks, Other Services
The ACLU interprets the establishment clause as forbidding any government funds going to religious schools, and the free exercise clause as guaranteeing the right of religious schools to exist. The former part includes a ban on lending any books or other instructional materials to religious schools; or any help with facilities; or bus services.
However, "hot lunches or public health services" can be directly provided (i.e. not through religious schools) by the government to all children, even those attending religious schools because these involve community concerns for children that exist separately from education.
The ACLU therefore also opposes voucher plans on the grounds that "[a]ny public aid to a religious school inevitably benefits the entire institution, regardless of the particular uses for which it is designated" and this would clearly go against the First Amendment. This includes any kind of tax benefits, even benefits commonly granted to parents who send their children to public schools.
Policy 80a — Church-State Task Force
This policy calls for the formation of an internal ACLU task force to track and respond to Church-State issues.
Policy 81 — Religion in Public Schools
Public schools may not indoctrinate children in religious beliefs, whether in an obvious or subtle manner. They distinguish "the teaching of religion" from "teaching factually about religion," where the latter may be appropriate for history and social science classes.
Regular Bible reading, organized prayers, teaching religious doctrines as if they were scientific, and celebrating Christmas, Channukah, or Easter as religious holidays are all methods of subtle indoctrination.
Public funds should not be used for displays of religious symbols. Nor should public facilities be used for religious purposes either during or after school hours. Public school teachers should not be allowed to wear "distinctively clerical garb," but religious belief or associations should never count against a teacher professionally.
Value education is important, but must be carried out in a secular way rather than as a "subterfuge" for introducing religious indoctrination.
Policy 82 — Shared Time
"Shared time" refers to students attending both public and religious schools, usually to pick up certain classes unavailable in the other context. This isn't necessarily unconstitutional, but does tend to result in public funding going to religious schools. In addition, it can give educators at religious schools some influence over public school operations, such as pressure to agree on common textbooks.
Policy 83 — Released Time
"Released time" is the practice of letting children choose to leave public school at certain times, but only to attend some form of religious instruction. This is quite different from simply releasing all students to do what they like, and so it encourages religious participation...and usually specific kinds of religious participation at that.
Released time also disrupts school for the other students and teachers who remain. For these reasons, the ACLU opposes it.
Policy 84 — Pledge of Allegiance
When the words "under God" were added to the Pledge of Allegiance in 1954, the ACLU held that the principle of separation of church and state was violated.
Students who have secular or religious reasons for not saluting the flag or swearing an oath of allegiance should be excused from any such requirement.
Policy 85 — Government Jurisdiction Over Parochial School Lay Teachers
Government intervention in the form of the National Labor Relations Board is not necessarily a problem for church/state separation.
Policy 86 — State Educational Standards
The ACLU opposes allowances for parents to opt their children out of public school classes they feel conflict with their religious beliefs, as this gives religious bodies indirect control over curriculum. This includes parents who would prefer to send their children to private schools but cannot afford it.
State educational standards — which cover both public and private schools — should make exceptions for religious schools in "right of conscience" cases, which occur when parents believe they themselves would be guilty of a great wrong for complying with the law. That is, unless the "safety, health, or welfare of the child" is put at risk.
Policy 87 — Higher Education
Colleges and universities which are sponsored by religious institutions but are not run in a way that promotes religions may be eligible for public funds. Nor does the inclusion of a seminary program disqualify rest of the institution from receiving public funds.
Practices which would disqualify the institution as a whole include: religious discrimination affecting faculty or students, any requirements to attend religious events, any courses which foster religion, any religious symbols intended to foster religion in buildings other than chapels, or prayers at any "institution-sponsored events."
Policy 88 — Military Chaplaincy
The ACLU believes the free exercise clause requires that members of the military have access to religious ministers of their own sect, and therefore that such ministers have access to members of the military.
However, the current (as of 1973 and from what I gather still current) form of the chaplaincy often discriminates against minority religious beliefs.
Policy 89 — Prison Chaplaincy
As with the military chaplaincy, there is a tendency to select only from the religious majority, without adjusting for the actual religious beliefs of those served. This combined with "the prominence accorded religious observance in evaluating a prisoner's success in conforming to the rehabilitative model at the core of the parole process" translates into an unconstitutional establishment of religion. Beyond parole, prison chaplains can often coerce religious participation through their influence on the institution.
For these reasons, the ACLU opposes the way prison chaplaincies are implemented. Prisoners should have free access to "a religious or ethical counselor of his or her choice" and such counselors must in turn be allowed to access prisoners.
Policy 89a — Privileged Communications with the Clergy
The ACLU believes the free exercise clause guarantees clergy the right not to be compelled during testimony to disclose information received in confidence in their professional role.
Policy 90 — Blue Laws
While the government may mandate a six day work week for secular reasons, special "Lord's Day" laws restricting behavior on Sundays for religious reasons violate the establishment clause.
Policy 91 — Marriage
Laws against plural marriage — marriage to more than one person — violate "constitutional protections of freedom of expression and association, freedom of religion, and privacy for personal relationships between consenting adults."
In cases of civil divorce, the government may not compel people to have their marriage dissolved by religious authorities.
Policy 92 — Religious Bodies' Tax Exemption
The ACLU considers tax benefits to be the equivalent of giving public funds to religious groups, and so opposes the practice.
However, benefits or funds may properly be given to charitable organizations sponsored by religious groups, so long as "religion plays no part in the delivery of such services" i.e: no religious message with the service, and neither workers nor recipients are subject to a religious test.
The ACLU opposes making exceptions for taxes — such as social security — for religious sects who claim conscientious objection. Slippery slope.
Policy 93 — Collection and Dissemination of Religious Information
During a census or similar state information gathering activities, the ACLU believes there are reasons for the government to ask about race, but not about religion. The main justification being that the state is not allowed to discriminate based on religion, but has an "affirmative obligation to act in order to combat massive discrimination" when it comes to race.
In fact, the government should not even record volunteered information about religious beliefs, except in special cases like military and prison chaplaincies.
Policy 94 — Non-Belief in a Supreme Being
The ACLU supports the Supreme Court's affirmation in Torcaso v. Watkins that state or federal office-holding may not be contingent on a confession of belief in a God.
Non-believers in a God also face unconstitutional discrimination when their conscientious objections to military service are ignored, whereas a privileged kind of religious belief would be respected.
Citizens — religious or not — who have an objection to swearing an oath to God must always be given the opportunity to 'affirm' their words rather than swear.
Policy 95 — Church Political Activities
Religious groups may be as involved in politics as any other groups of citizens.
Policy 96 — Charitable Contributions by Private Utility Companies
If utility rates are increased for citizens because a private utility company is donating to religious causes, the ACLU will object. This is effectively a form of taxation.
Policy 97 — Public Assistance to Members of Religious Orders
Being a member of a religious order should not disqualify a citizen for welfare or other government services that would otherwise be due to them. This is the flip-side to the ACLU opposing special positive state treatment for the clergy.
Policy 98 — Government Funding of Social Service Programs of Religious Bodies
In general, state funds may not go to social programs sponsored by religious groups. It may be appropriate in special cases where these services are rendered without any mention or sign of religion and in a non-discriminatory way.
Policy 99 — Use of Public Property for Religious Purposes
Public property which is known to be open for anyone's use as a public forum may, of course, be used to express religious ideas without any implication of government endorsement. So public parks and streets may be used for religious purposes, but the same sorts of things in most government administrative buildings would be — or would be perceived to be — state endorsement of religion.
The ACLU considers public school buildings to be among the kind of government buildings which cannot allow any religious activities (even "student initiated religious clubs"), at least not during school hours or immediately adjacent to them. "The school is inextricably linked with religious activities if it sanctions religious clubs." For this reason, the ACLU believes the Equal Access Act is "a flagrant violation of the Establishment Clause" and should be repealed.
UPDATE: I did some Googling; it appears the ACLU now frequently invokes the Equal Access Act because it's so helpful in starting Gay/Straight Alliance clubs.
Policy 100 — Governmental Use of Religious Organizations for Overseas Relief Programs
Secular programs should be used instead whenever possible. Religious channels may be used to deliver emergency aid when necessary if the public funds only apply to secular aspects of the relief program, proselytism is contractually forbidden while the religious group is distributing public benefits, and there is no religious test for those receiving or distributing benefits.
Policy 101 — Kidnapping Young People from Religious Groups
In lieu of physical coercion or threats of physical coercion, the government may not remove people from religious groups on grounds of "brainwashing." This is obviously meant to apply to small religious movements considered to be "cults."
Policy 102 — Diplomatic Relations with the Vatican
The ACLU is opposed to the United States establishing a "formal diplomatic relationship with the Holy See," since this is a level of official recognition of a religious authority not afforded to other religious groups.