MySQL is not using the index for queries, I caught it doing table scans while a host is applying it's manifests:
(localhost) [foreman]> explain SELECT * FROM sources WHERE value = '//darts.foo.bar/Puppet';
---------------+---------+------+---------------+------+---------+------+--------+-------------+ | id | select_type | table | type | possible_keys | key | key_len | ref | rows | Extra |
---------------+---------+------+---------------+------+---------+------+--------+-------------+ | 1 | SIMPLE | sources | ALL | value | NULL | NULL | NULL | 140037 | Using where |
---------------+---------+------+---------------+------+---------+------+--------+-------------+
1 row in set (0.00 sec)

(localhost) [foreman]> show create table sources;
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | Table | Create Table |
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | sources | CREATE TABLE `sources` (
`id` int(11) NOT NULL AUTO_INCREMENT,
`value` text,
PRIMARY KEY (`id`),
FULLTEXT KEY `value` (`value`)
) ENGINE=MyISAM AUTO_INCREMENT=295256 DEFAULT CHARSET=latin1 |
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
1 row in set (0.00 sec)

(localhost) [foreman]> show indexes from sources;
-------------------+----------+--------------+-------------+-----------+-------------+----------+--------+------+------------+---------+ | Table | Non_unique | Key_name | Seq_in_index | Column_name | Collation | Cardinality | Sub_part | Packed | Null | Index_type | Comment |
-------------------+----------+--------------+-------------+-----------+-------------+----------+--------+------+------------+---------+ | sources | 0 | PRIMARY | 1 | id | A | 122065 | NULL | NULL | | BTREE | | | sources | 1 | value | 1 | value | NULL | NULL | NULL | NULL | YES | FULLTEXT | |
-------------------+----------+--------------+-------------+-----------+-------------+----------+--------+------+------------+---------+
2 rows in set (0.00 sec)

In the schema.rb:
create_table "sources", :force => true do |t|
t.text "value"
end

add_index "sources", ["value"], :name => "value"

This appears to create a fulltext index for the sources.value column in foreman's db.

Adding a non fulltext-type index solves this, I added an index for the first 120 characters to speed things up.
(localhost) [foreman]> create index index_sources_value on sources(value(120));
Query OK, 140705 rows affected (5.46 sec)
Records: 140705 Duplicates: 0 Warnings: 0

(localhost) [foreman]> explain SELECT * FROM sources WHERE value = '//darts.foo.bar/Puppet';
---------------+---------+------+--------------------+--------------+---------+-------+------+-------------+ | id | select_type | table | type | possible_keys | key | key_len | ref | rows | Extra |
---------------+---------+------+--------------------+--------------+---------+-------+------+-------------+ | 1 | SIMPLE | sources | ref | sourcevalues,value | sourcevalues | 123 | const | 1 | Using where |
---------------+---------+------+--------------------+--------------+---------+-------+------+-------------+
1 row in set (0.00 sec)

I love this project, wanted to contribute something back that I'd experienced today.