(The translations following each term are my own, and my Latin is highly limited, so they may be imprecise. Feel free to let me know if you have a better translation.)
Amicabilis compositio (amicable composition): the means allotted for resolving religious disputes in the Diet (IPO Art. V,52), instead of by a simple vote. The term is used in several other places in the treaties, where the details of certain disputes are referred to this as a means of settling matters between disputants.
Corpus Catholicorum (the body of Catholics, i.e. the Catholic body): All Catholic estates in the Empire, considered as one party. “Itio in partes” refers to the estates dividing into parts by religion, of which this is one.
Corpus Evangelicorum (the body of Protestants): All Protestant estates in the Empire (including Calvinists), considered as one party. The IPO does not use this term directly, but it speaks of cases where “the estates cannot be considered a single body” they will divide into two parties (IPO V, 52).
Cuius regio, eius religio
Dominium maris Baltici
Effectus suspensivus (effective suspension): The Emperor (Ferdinand III) agreed to a new amnesty at the Diet of Regensburg in 1640, pardoning all those who had been at war with him. However, the amnesty was only to take effect once all Imperial estates had agreed to rejoin the Emperor in the fight against foreign powers; until then, it was “effectively suspended,” meaning that any estate that did not benefit from a previous amnesty would not benefit from the Regensburg amnesty. The Emperor finally agreed to life the effectus suspensivus in 1645 as a condition of negotiations.
Foederum ius (right of alliances): the right of Imperial estates to make alliances with foreign powers, which successive Emperors had disputed. it is not mentioned by name in the Peace of Westphalia, but it is stated clearly in the IPO, Art. VIII,2 and IPM § 63.
Gravamina ecclesiastica (religious grivances): complaints about various religious affairs in the Empire, mostly on the part of Protestants, but also by Catholics. The Peace of Westphalia set out to resolve these grievances (IPO Art. VII,1).
Gravamina politica (political grievances): complaints by Imperial estates about political arrangements in the Empire. These are not mentioned by the name gravamina politica in the treaties, but they are understood to be resolved by changes to the Imperial constiution.
Instrumentum Pacis Monasteriensis (peace document of Münster): the document signed by the representatives of the Empire and France on October 24, 1648. It is not technically a separate treaty, because it is declared to be part of a single peace treaty along with the Instrumentum Pacis Osnabrugensis. The “Treaty of Münster” usually refers to the Spanish-Dutch peace treaty of the same year. References to this particular document often use the abbreviation IPM.
Instrumentum Pacis Osnabrugensis (peace document of Osnabrück): the document signed by the representatives of the Empire and Sweden on October 24, 1648. Note that it was actually signed in Münster, not Osnabrück, so as to co-ordinate with the signing of the IPM. Often abbreviated as IPO. (See the summary and text here.)
Itio in partes (going into parts, or dividing into parties): in religious matters in the Diet, members were to divide into their parties (Protestant — Corpus Evangelicorum — and Catholic — Corpus Catholicorum) to debate among themselves, and then reach an amicable composition (amicabilis compositio).
Ius pacis et belli (right of peace and war): the right of Imperial estates to have a say in matters of making peace and war. Not mentioned in these words, but declared in similar terms in IPO VIII, 2. Not to be confused with the book written by Hugo Grotius in 1624, De Iure Belli Ac Pacis (Of the Right of War and Peace).
Ius emigrandi (right of emigrating): The right granted to members of a minority faith to leave a territory and dispose of their goods or leave them to be administered by someone else. They are allowed at least five years to leave if they converted prior to the signing of the peace, three years if following (IPO V, 36-37).
Ius reformandi (right of reformation): The right of the ruler of a territory to convert the official church of his land to one of the accepted faiths (Catholic, Lutheran, or Calvinist). It is mentioned explicitly in IPO V, 29 regarding Imperial Free Cities, whose right to reform their surrounding territories (as well as the area inside city walls) is confirmed. It is implicitly confirmed for Imperial Knights in IPO V, 28, where they are confirmed “in the rights concerning religion” that other estates have.
Ius suffragii (voting right): the right of Imperial estates to vote in all Imperial matters, listed in IPO VIII, 2.
Nondum reconciliati (not yet reconciled): Those estates which had not accepted the Peace of Prague, or which had accepted it but not been re-instated in their lands because of the effectus suspensivus.
Privilegium de non appellando (privilege of not appealing): A right granted to some Imperial estates that their judicial decisions could not be appealed to the Emperor. Sweden was accorded this privilege for its Imperial territories. (France, which removed its conquests from the Empire, had no need for it.)
Satisfactio coronae (satisfaction of the crown): The term for compensation to be given to Sweden or France for their efforts in the war. “Satisfactio” is used in this sense in the IPM (§ 106). In the IPO, it is used when discussing Mecklenburg’s compensation (XII, 3-4) and to emphasize that Sweden will not demand compensation for the lands it returns (XVI, 14).