MacOS – What Lion maintenance utility should I use

Are there Mac equivalents that monitor startup, configuration and the like?

OnyX, Snow Leopard Cache Cleaner, iTweax are some options.

How necessary are they?

Not very. Any optimization that needs to be done is already built into the Mac OS X.

What is the best general purpose package?

Can't help you there, I don't use such utilities.

No, I don't think so. Spotlight indexes files in order for quick searching. Once indexed, a file is very quick to find, the part that takes time is the actual indexing. I suppose you could argue that the act of moving a file might cause it to be re-indexed (now that it's in a new location), but I don't know enough about how Spotlight works to be sure. Either way, the difference you would notice would be minimal. Once the initial indexing is done, the time spent adjusting the indexes is not big.