The bare minimum for an fpga design to run standalone:
1. Power supplies (I/O voltages of maybe 3.3/1.8/2.5, analog PLL supplies 2.5v, Vcore 1.2v or 1.1v)
2. Clock source (50mhz LVCMOS oscillator is common)
3. Config storage (usually SPI flash rom)
Altera's EPCS chips are just remarked ST/Numonyx flash roms. If you are careful about what specs parts you get you can find a drop-in commodity replacement.
FPGAs generally have builtin self-configuration circuitry. They have a rough internal oscillator, enough to clock in bits from the external SPI rom.
They will also have a variety of other configuration schemes, fast parallel, fast serial (QSPI), etc... It depends if you need to re-configure the FPGA on the fly to swap operating modes often, or just send updates in the field.
For lowest PLL jitter at the very least put a pi filter on the Vcca supplies, you can use a switching regulator fine.
Low-demand fpga boards can get by with just a few LDOs.
For low voltage, high current core voltages like 1v2, use a push pull converter instead of the classical buck converter. I use the semtech SC185, switching speed is 1Mhz and uses cheap small passives. For high speed switching regs like this you will want to use MLCC caps, not alum. electrolytic because of their lower ESR.
Anyway that's the real bog-standard stuff, more specific applications will come with more specific requirements.