In necessariis unitas, in non necessariis libertas, in utrisque caritas (Marco Antonio De Dominis, 1617). Cf. In necessariis unitas, in dubiis libertas, in omnibus caritas (and other variants). English: "In essentials unity. . . ."

The earliest known occurrence of this so far is to my knowledge once again "Catholic", if somewhat dubiously so, given that the Dictionnaire de théologie catholique calls the De republica ecclesiastica "a very interesting blend of theses Anglican and Gallican" (vol. 4, col. 1670), and the 2nd edition of the New Catholic encyclopedia, De Dominis himself an "apostate":

In preparing vol. XVII of the Briefwisseling van Hugo Grotius I came across a letter which the French scholar Jean de Cordes addressed to Grotius on 9 November 1634 (Bodleian Library, Oxford, MS. D'Orville 51).  In this letter the source of the adage is mentioned, be it rather vaguely:  the works of Marc' Antonio de Dominis (1560-1624), archbishop of Split (Spalato).  After some research I have found the device in book 4, chapter 8 of De republica ecclesiastica libri X, London/Hannover 1617-1622)

i.e. “on p. 676 of the first volume published in London in 1617, at the end of chapter 8 of book 4, which treats of the papacy” (H. J. M. Nellen, "De zinspreuk 'In necessariis unitas, in non necessariis libertas, in utrisque caritas,'" Nederlands archief voor kerkgeschidenis 79, no. 1 (1999): 106, 104 (99-106)).  Cf. http://spu.worldcat.org/title/marci-antonii-de-dominis-de-republica-ecclesiastica-libri-x/oclc/476586221.  On p. 104 of this article it appears as follows:

Quod si in ipsa radice, hoc est sede, vel potius solio Romani pontificis haec abominationis lues purgaretur et ex communi ecclesiae consilio consensuque auferretur hic metus, depressa scilicet hac petra scandali ac ad normae canonicae iustitiam complanata, haberemus ecclesiae atrium aequabile levigatum ac pulcherrimis sanctuarii gemmis splendidissimum. Omnesque mutuam amplecteremur unitatem in necessariis, in non necessariis libertatem, in omnibus caritatem. Ita sentio, ita opto, ita plane spero, in eo qui est spes nostra et non confundemur.

Now if this plague of an abomination [were to] be cleared away at the root—i.e. see or rather throne of the Roman pontiff—itself, and [if] that fear hanging over the common counsel and consent of the Church (suppressed, of course, by this stone that makes men stumble [(cf. 1 Pet 2:8 in the Vulgate)], and reduced to the ‘equity’ of canon law) [were to] be removed, we would have an equitable atrium of the Church polished and [rendered] surpassingly brilliant by the beautiful gems of the sanctuary. And we would all embrace a mutual unity in things necessary; in things non necessary liberty; in all things charity. This I feel, this I desire, this I do indeed hope for, in him who is our hope and we are not confounded.

It appears in ll. 3 and 2 from the very bottom of p. 676 of the book itself as follows:

vnitatem in necessarijs, in non necessarijs libertatem, in omnibus caritatem.

I would welcome any suggestions for the refinement of the translation I give above.

This was quoted by De Cordes (who claimed to "ay trouvé [it] dans les oeuvres de Dominis") in his letter to Grotius dated 9 November 1634 (above) as follows:

in necessariis unitas, in non necessariis libertas et in omnibus charitas

(Nellen, 102).  Grotius knew De Dominis personally, and, indeed, was in possession of this first volume of the De republica ecclesiastica by 1619 (Nellen, 103).  But he wouldn't have been able to track the maxim down on the strength of this vague reference alone (Nellen, 104).

For additional passages in De Dominis' De republica ecclesiastica that give voice to similar sentiments, see Nellen, 104n20:  bk. 7, chap. 6, sec. 21 (p. 104); bk. 7, chap. 9, sec. 18 (p. 130); bk. 7, chap. 9, sec. 27 (p. 132); bk. 7, chap. 9, sec. 204 (p. 197); bk. 7, chap. 12, sec. 113 (p. 316).

Would the presence of De Dominis in England go some way towards accounting for the major role played by Richard Baxter (1615-1691) in the dissemination of the maxim several decades later?  "The apostacy [(geloofsafval)] of the Archbishop and his flirtation with Anglicanism made him for representatives of the Reformation an important trump card in the religious controversy with Rome" (Nellen, 105)—for as long, at least, as that flirtation lasted.  And quite probably longer.

Prior to this ground-breaking article by Nellen (which, he admits, may well be superceded by "the definitive answer" published "in 2065—or perhaps much earlier" (Nellen, 101)), the consensus of more than a century had been that it was the work of Peter Meiderlin (1582-1651) (anagrammatico-pseudonymously Rupertus Meldenius), and appeared for the very first time in the first (i.e. 1626) printing of his Paraenesis votiva pro pace ecclesiae ad theologos Augustanae Confessionis  (http://spu.worldcat.org/title/paraenesis-votiva-pro-pace-ecclesiae-ad-theologos-augustanae-confessionis/oclc/34765422):

Verbo dicam: si nos servaremus in necessariis unitatem, in non necessariis libertatem, in utrisque caritatem, optimo certe loco essent res nostrae.

(Meiderlin's Paraenesis was so rare that Friedrich Lücke reproduced it in an appendix to his Über das Alter, den Verfasser, die ursprüngliche Form und den wahren Sinn des kirchlichen Friedenssprüches "In necessariis unitas, in non necessariis libertas, in utrisque caritas":  eine literar-historische theologische Studie (Göttingen:  Dieterich, 1850).)

"Meiderlin is [therefore] a disciple of Johann Arndt, but he seeks less to defend the ideas of his master (in whom one can see a precursor of 'Pietism') than to bring an end to the dogmatic rivalries of the theologians of the Augsburg Confession" (Joseph Lecler, "À propos d'une maxime citée par le Pape Jean XXIII: In necessariis unitas, in dubiis libertas, in omnibus caritas," Recherches de science religieuse 49 (1961): 552 (549-560)).

In Catholic (but also some Protestant) hands, dubiis was substituted for non necessariis [(note also the presence of omnibus rather than, as in Meiderlin, utrisque)], and this had supposedly the effect of extending "the rule of Meldenius . . . to much more than just the necessaria [(for salvation)] and the non necessaria [(for salvation)]", much more than just the "fundamental articles":  "the tripartite maxim. . . . [thus] lost its original Protestant nuance, in order to extend liberty to the entire domain of questions debated, doubtful, and undefined [(non définies par l'Église)]" (Lecler, 559-560).  There are many helpful references to the literature (but most notably Krüger and Eekhof) in Lecler, who isn't doing much in the way of original scholarship, but mostly summarizing the work of others (Eekhof and Krüger, and, for more than a century total behind them, Bauer, Lücke, and Morin).

But the 1999 article by Nellen has, for now at least, returned this once again to (a dubious) "Catholicism".

"In necessariis unitas, | in dubiis libertas, | in omnibus caritas. | Augustin, dem John Wesley | zugestimmt hätte. | Geoffrey Wainwright | in herrlicher Verbundenheit. | Manfred Marquardt | Cambridge, July 24th,1987".  Inscription on title page of a copy of Praxis und Prinzipien der Sozialethic John Wesleys, by Manfred Marquardt (Göttingen:  Vandenhoeck & Ruprecht, 1977), purchased from Windows Booksellers for the Seattle Pacific University Library on 9 July 2014.  "Augustine, with whom John Wesley would have agreed.  [To] Geoffrey Wainwright", etc.

Here is a bit more in the way of 20th- and 21-century bibliography, thrown in quite willy nilly as encountered (rather than searched for) after I first posted this on 2 March 2010.  I do not claim to have read all that follows, nor that this list is anything even close to exhaustive.

• Moravian Archives, Bethlehem, PA.  "And in all things . . ."  This month in Moravian history no. 73 (May 2012).  Cites Comenius' Unum necessarium (1668):  "Servare in omnino necessariis Unitatem:  in minus necessarius (qva Adiaphora vocant) Libertatem:  in omnibus erga omnes Charitatem."  
• Rollmann, Hans. "In essentials unity:  the pre-history of a Restoration Movement slogan."  Restoration quarterly 39 (1997):  129-139.  Credits Peter Meiderlin.
• Burr, Viktor.  "Zur Geschichte des Wahlspruches:  In necessariis unitas, in dubiis libertas, in omnibus caritas."  In 110 Jahre Unitas-Salia zu Bonn/1847 bis 1957 - Festschrift zum 110. Stiftungsfest des W.K.St.V. Unitas-Salia, der Mutterkorporation des Unitas-Verbandes, edited by Anton Brenig, 7-24.  Bonn, 1957.

And here is a grab-bag of allusions, thrown in (here, too) quite willy nilly as encountered:

"All in the church must preserve unity in essentials [(In necessariis unitatem)].  But let all, according to the gifts they have received, maintain a proper freedom [(debitam libertatem)] in their various forms of spiritual life and discipline, in their different liturgical rites, and even in their theological elaborations of revealed truth.   In all things let charity [(in omnibus . . . caritatem)] prevail.  If they are true to this course of action, they will be giving ever better expression to the authentic catholicity and apostolicity of the church" (Unitatis redintegratio 1.4; Decrees, ed. Tanner, vol. 2. p. 912).