Assuming you know that the subjunctive is required, a simplified rule for determining which subjunctive tense to use is as follows:

With a governing verb in a “present time” tense use only a “present time” tense of the subjunctive; with a governing verb in a “past time” tense, use only a “past time” subjunctive. In either case the simple subjunctive tense is used to express a simultaneous or future action, and the perfect tense is used to indicate a previous activity.

Situation 1

When the governing verb is in a “present time” tense use one of these tenses when the subjunctive is required:

• present indicative present subjunctive [for a simultaneous or future state or future action]
• future indicative
• imperative (command)
• present perfect indicative OR
• future perfect indicative present perfect subjunctive [for a prior state or action {or the imperfect subjunctive where the imperfect indicative would otherwise be used}]
• present subjunctive
• present perfect subjunctive

Examples:

• Dudo que vengan. I doubt that they are coming [right now].

I doubt that they will come [in the future].
Governing verb: Dudo (present indicative)
Subordinate verb: vengan (present subjunctive to indicate a simultaneous or future event)

• Dudo que hayan venido. I doubt that they came [in the past].

I doubt that they have come.
Governing verb: Dudo (present indicative)
Subordinate verb: hayan venido (present perfect subjunctive to indicate a previous event)

Situation 2

When the governing verb in a “past time” tense use one of these tenses when the subjunctive is required:

• imperfect indicative imperfect subjunctive [for a simultaneous or future state or action]
• preterit indicative
• conditional OR
• conditional perfect past perfect subjunctive [for a prior state or action]
• imperfect subjunctive
• past perfect subjunctive

Examples:

• Dudaba que vinieran. I doubted that they were coming [right then].

I doubted that they would come [in the future].
Governing verb: Dudaba (imperfect indicative)
Subordinate verb: vinieran (past subjunctive to indicate a simultaneous or future event)

• Dudaba que hubieran venido. I doubted that they had come [earlier].

Governing verb: Dudaba (imperfect indicative)
Subordinate verb: hubieran venido (past perfect subjunctive to indicate a previous event)

Expanded version of the above simplified rule:

When a governing verb in the present, future, or future perfect tense and the subjunctive is required in a subordinate clause, use the present or present perfect subjunctive; with a governing verb in a “past time” tense —imperfect, preterit, past perfect, conditional, or conditional perfect—, use only a “past time” subjunctive: imperfect or past perfect. In either case the simple subjunctive tense (present for “present time”, or imperfect for “past time”) is used to express a simultaneous or future action, and the perfect tense (present perfect for “present time”, or past perfect for “past time”) is used to indicate a previous activity.

REMINDER: When the governing verb is in a past tenses and the subjunctive is required, a past subjunctive is almost always used. The conditional is considered a past tense..

Special situations involving the past subjunctives.

1. Como si (“as if”) MUST be followed by a past subjunctive:

• El habla como si fuera rico.
  He talks as if he were rich.
• Ella habla como si hubiera vivido en México.
  She talks as if she has (had) lived in Mexico.

2. Ojalá and the subjunctive. Ojalá plus the present subjunctive is used in the sense of “I hope”; with a past subjunctive, it means “I wish”, and implies that something is hypothetical or contrary-to-fact:

• Ojalá que esté aquí.
  I hope she's here. [She might be here.]
• Ojalá que haya estado aquí.
  I hope she's been here. [She may have been here.]
• Ojalá que estuviera aquí.
  I wish she were here. [She's not here.]
• Ojalá que hubiera estado aquí.
  I wish she had been here. [She has not been here.]