The shadow memory options (Video BIOS Shadow, C800-CFFF Shadow, etc.) are used to put the respective ROM memory addresses into 'shadow RAM', a special portion of memory set aside by the motherboard's memory controller. (This is not related to cache memory; shadow RAM is a portion of your DRAM set aside for such a purpose.) The reason for wanting to do this is to increase performance of any ROMs that may be located in said memory spaces, as RAM is usually much faster than ROM. Sometimes this causes some problems when you try to update the BIOS of said cards with ROM chips in the respective ranges, so you can manually disable shadowing for these regions when need be.
ISA I/O Recovery adds wait states to accesses to the ISA bus, which may help cure things like lockups, data corruption, weird glitches, etc. when using a CPU that is a bit faster than certain ISA cards may like to talk to. (I'm thinking of cards with Yamaha OPL3 FM synthesis chips, though sometimes ISA network cards need a little extra time as well.) On a fairly fast system like the one you've got, there will typically be little observable difference in performance with this enabled or disabled, so don't be too quick to turn it off if it's already on.
Generally you'd want PCI Fast Back-to-Back Transaction enabled, unless you run into glitchiness with PCI video or SCSI cards.
Hidden Refresh tells the motherboard's memory controller to handle memory refresh without bothering the CPU about it. With this off, the CPU has periodically drop whatever it's doing to to refresh the memory in the system, which can eat a fair bit of the CPU's time. Basically enabling this improves performance, though if you're trying to use memory chips that aren't really up to the speed you're running the CPU bus at (say, trying to run 70ns chips on a 60 or 66MHz Pentium FSB) then enabling this will increase the chance of you running into memory errors. Also some marginal motherboard chipsets don't necessarily do a good job of this so you may have to disable this even if the memory seems fast enough to work otherwise. Usually you can leave this enabled though.
HDD Block Mode is a performance enhancing feature for the IDE hard drive, which enables multiple-sector transfers to the HDD(s) connected to the IDE channel(s). Some really old IDE hard drives and early builds of Windows 95 (pre-OSR2 mainly) and OS/2 sometimes didn't work well with block mode transfers during setup, so the manufacturers allowed this to be disabled when needed.
CPU to PCI write buffer should be ON. That enables a FIFO buffer of sorts between the CPU and PCI interface and will improve performance.
CPU to PCI Byte Merge is another performance enhancing function, I don't know exactly how it works but generally you leave that on unless you get weird problems with video or network cards.
PCI to DRAM Buffer should be ON. Similar with the CPU to PCI write buffer, except this enables a FIFO buffer between the PCI bus and memory controller. Only turn this off if you run into weird problems.
Life isn't long enough to re-enable every hidden option in every BIOS on every board... 🙁