In SQLAlchemy, how do I populate or update a table from a SELECT statement?

SQLalchemy doesn’t build this construct for you. You can use the query from text.

session.execute('INSERT INTO t1 (SELECT * FROM t2)')

EDIT:

More than one year later, but now on sqlalchemy 0.6+ you can create it:

from sqlalchemy.ext import compiler
from sqlalchemy.sql.expression import Executable, ClauseElement

class InsertFromSelect(Executable, ClauseElement):
    def __init__(self, table, select):
        self.table = table
        self.select = select

@compiler.compiles(InsertFromSelect)
def visit_insert_from_select(element, compiler, **kw):
    return "INSERT INTO %s (%s)" % (
        compiler.process(element.table, asfrom=True),
        compiler.process(element.select)
    )

insert = InsertFromSelect(t1, select([t1]).where(t1.c.x>5))
print insert

Produces:

"INSERT INTO mytable (SELECT mytable.x, mytable.y, mytable.z FROM mytable WHERE mytable.x > :x_1)"

Another EDIT:

Now, 4 years later, the syntax is incorporated in SQLAlchemy 0.9, and backported to 0.8.3; You can create any select() and then use the new from_select() method of Insert objects:

>>> from sqlalchemy.sql import table, column
>>> t1 = table('t1', column('a'), column('b'))
>>> t2 = table('t2', column('x'), column('y'))
>>> print(t1.insert().from_select(['a', 'b'], t2.select().where(t2.c.y == 5)))
INSERT INTO t1 (a, b) SELECT t2.x, t2.y
FROM t2
WHERE t2.y = :y_1

More information in the docs.

As of 0.8.3, you can now do this directly in sqlalchemy: Insert.from_select:

sel = select([table1.c.a, table1.c.b]).where(table1.c.c > 5)
ins = table2.insert().from_select(['a', 'b'], sel)

As Noslko pointed out in comment, you can now get rid of raw sql:
http://www.sqlalchemy.org/docs/core/compiler.html#compiling-sub-elements-of-a-custom-expression-construct

from sqlalchemy.ext.compiler import compiles
from sqlalchemy.sql.expression import Executable, ClauseElement

class InsertFromSelect(Executable, ClauseElement):
    def __init__(self, table, select):
        self.table = table
        self.select = select

@compiles(InsertFromSelect)
def visit_insert_from_select(element, compiler, **kw):
    return "INSERT INTO %s (%s)" % (
        compiler.process(element.table, asfrom=True),
        compiler.process(element.select)
    )

insert = InsertFromSelect(t1, select([t1]).where(t1.c.x>5))
print insert

Produces:

INSERT INTO mytable (SELECT mytable.x, mytable.y, mytable.z FROM mytable WHERE mytable.x > :x_1)