Anne Mahoney, Overview of Latin Syntax

Subjunctive

Clauses with “cum” take the subjunctive when the “cum-”clause tells something about the circumstances around the main action. AG 546

• “Cum civitas ob eam rem incitata armis ius suum exsequi conaretur, Orgetorix mortuus est, neque abest suspicio quin ipse sibi mortem consciverit.” Caesar, BG 1.4. Here Caesar's use of the subjunctive means that Orgetorix died not just while the Helvetians were preparing to fight him, but because they'd turned against him — as the next clause makes clear.
• “Quid facient crines, cum ferro talia cedant?” Catullus 66.47
• “At studuit Catilinae, cum iam aliquot annos esset in foro, Caelius.” Cicero, Cael. 12 If Cicero had said “fuit”, he would simply have been indicating the time when Caelius took up with Catiline. “Esset” means that Caelius's several years of experience in the Forum are relevant: Caelius had already begun to establish himself as a competent, steady young man.

Concessive and causal “cum-”clauses also take the subjunctive. AG 549

• “Haedui, cum se suaque ab eis defendere non possent, legatos ad Caesarem mittunt.” Caesar, BG 1.11. Because the Haedui could not defend themselves...
• “Quod cum ita sit, nolim statuas nos mente maligna id facere.” Catullus 68.37

Subordinate clauses in indirect discourse take the subjunctive, though clauses that are not actually part of the quotation take the same mood as they would in direct discourse. AG 580, 585

• “His Caesar ita respondit: eo sibi minus dubitationis dari quod eas res, quas legati Helvetii commemorassent, memoria teneret.” Caesar, BG 1.14.
• “Cum a me quoque id responsum tulisses, me nullo modo posse isdem parietibus tuto esse tecum, quia magno in periculo essem quod isdem moenibus contineremur, ad Q. Metellum praetorem venisti.” Cicero, Catil. 1.19 Both of the "because" clauses are part of the response Catiline got from Cicero.

Indirect questions take the subjunctive. AG 574

• “Eodem die qualis esset natura montis exploratores qui cognoscerent misit.” Caesar, BG 1.21
• “Quare id faciam fortasse requiris.” Catullus 85.1

• “Quaeris quot mihi basiationes
  tuae, Lesbia, sint satis superque.
  

  ”

  Catullus 7.1-2

Conditional sentences take the subjunctive when the protasis is false; these are "contrary to fact" conditionals. "Future less vivid" conditionals, where the protasis gives a supposition or hypothesis that might or might not be true, also use the subjunctive. Sometimes general or "whenever" conditionals take the subjunctive, but these may also be treated as simple conditionals. AG 514, 516, 517, 518

• “Nostri, si ab illis initium transeundi fieret, parati in armis erant.” Caesar, BG 2.9 Our troops were ready in case theirs might begin to cross. The protasis is a hypothesis and the apodosis a fact; the protasis uses the imperfect subjunctive for subsequent action in secondary sequence.
• “Si nostri oblita taceret, sana esset.” Catullus 83.3-4 If Lesbia will forget about us and be quiet (which is not what she is doing), she will be OK (but instead she's going to fall in love). The protasis and apodosis are both contrary to fact; the imperfect subjunctive is used for continuing action, because the entire poem is cast in the present tense (cf. “dicit”, line 1).

Purpose clauses, sometimes called "final" clauses, take the subjunctive. AG 531

• “Frumentum omne comburunt, ut paratiores ad omnia pericula subeunda essent.” Caesar, BG 1.5.
• “Advenio ut te postremo donarem munere mortis.” Catullus 101.3
• “Maia genitum demittit ut terrae pateant hospitio Teucris.” Virgil, Aen. 1.297-299

Result clauses, sometimes called "consecutive" clauses, take the subjunctive. AG 537

• “His rebus fiebat ut minus facile finitimis bellum inferre possent.” Caesar, BG 1.2.

• “Atque illinc abii tuo lepore
  incensus, Licini, facetiisque,
  ut nec me miserum cibus iuvaret
  nec somnus tegeret quiete ocellos.
  

  ”

  Catullus 50.7-9

Relative clauses "of characteristic" also take the subjunctive; these give a general rule characterizing the antecedent. AG 534-535

• “Erant omnino itinera duo, quibus itineribus domo exire possent.” Caesar, BG 1.6 These are the sort of paths along which they could leave, paths suitable for leaving.
• “Quam diu quisquam erit qui te defendere audeat, vives.” Cicero, Catil. 1.6 Roughly, "So long as there is anyone to defend you, you will live." If Cicero had said “audebit”, that is all he would have meant; with the subjunctive, he means "anyone of the type of person who would stick up for you" — not a type of person for whom Cicero has much regard.

Relative clauses can take the subjunctive when they are equivalent to purpose clauses; here “qui” is equivalent to “ut is”. AG 531

• “Eodem die qualis esset natura montis exploratores qui cognoscerent misit.” Caesar, BG 1.21

• “Tam te basia multa basiare
  vesano satis et super Catullo est,
  quae nec pernumerare curiosi
  possint nec mala fascinare lingua.
  

  ”

  Catullus 7.9-12

The subjunctive can also be used in independent clauses, though this is relatively rare. Independent clauses with the subjunctive include commands ("hortatory" or "jussive" subjunctive, AG 439-440), wishes ("optative" subjunctive, AG 441-442), or doubtful questions ("deliberative" subjunctive, AG 444).

• “Miser Catulle, desinas ineptire.” Catullus 8.1
• “Qua re secedant improbi, secernant se a bonis, unum in locum congregentur, muro denique, quod saepe iam dixi, secernantur a nobis.” Cicero, Catil. 1.32

Negative commands are also independent clauses with the subjunctive, except of course those that use “noli” with the infinitive. AG 450

• “Nupta, tu quoque quae tuus
  vir petit cave ne neges
  

  ”

  Catullus 61.151-152