Gd punishing for not fulfilling a potential positive commandment: Kiddushin 39b [2x]; Menachot 41a
Ha'oseik b'mitzvah patur min hamitzvah העוסק במצוה פטור מן המצוה - one who is performing a mitzvah is exempt from other mitzvot
If one is already performing Mitzvah X, he is exempt from Mitzvah Y: Berachot 11a, 16a-b, 19a; Pesachim 55a; Succah 10b, 25a-26a; Ketuvot 6b; Nedarim 33b-34a
The Source for this principle: Succah 25a-b
We avoid creating such a conflict, if possible: Berachot 19a
Requiring that the commandment be fulfilled with the violation of the prohibition, immediately, in order for the commandment to override the prohibition: Shabbat 132b; Beitzah 8b
A commandment vs. a prohibition where both the commandment and the prohibition can be fulfilled: Shabbat 133a; Ketuvot 40a; Kiddushin 40a
A commandment with a punishment of Divine Ex-Communication, vs. an ordinary commandment: Pesachim 59a; Zevachim 32b
Where one of the mitzvot could be fulfilled by another individual: Berachot 14b; Kiddushin 32a
Where one mitzvah is more central to an act than the other is: Succah 56a
Whether the more common mitzvah ["Tadir"] has precedence: Succah 54b, 56a; Pesachim 114a; Megillah 29b; Menachot 49a
Whether the mitzvah involving a holier entity has precedence: Menachot 49a
Gauging which mitzvah to perform, if one involves a holier item, and the other is more common: Menachot 49a-b