I took a car from the Orphans' Fund Development Institution; is there usury (Riba) involved in this transaction?

If the Sharia's conditions were met, then there is no harm in this. And Allah The Exalted Knows Best.

Is it disliked to clip one`s nails at night, and to burn them afterwards?

It is recommended to bury hair and nails that have been removed and to conceal them in the ground. As for burning nails, we have not found any specific prohibition against it, but adhering to what is supported by evidence—burying the nails—is preferable. And Allah Knows Best.

Is it permissible to fish on Saturday?

All Perfect Praise be to Allah, The Lord of The Worlds, and may His Peace and Blessings be upon our Prophet Muhammad and upon all of his family and companions. 

It is permissible for Muslims to fish on any day, but the sons of Israel are the ones forbidden to fish on Saturday. Moreover, there is no evidence in Islamic Sharia prohibiting Muslims from fishing on that day. And Allah Knows Best.

Is it permissible to make up missed prayers at the times in which praying is disliked?

All perfect praise be to Allah,The Lord of The Worlds                                                                                                                                                                        It is permissible to make up missed prayers at any time even that in which praying is disliked. Absolute supererogatory prayer is forbidden to be performed at the times in which praying is disliked, and this also applies to Ihram and Istikhara prayers. However, there is no harm in offering prayers in Mekah during those times. And Allah Knows Best.