Software Alternative to RAID for Home Use

RAID1 is exactly what you want. Buy a well known controller card so if it craps out you can replace it. That way:

1. Hard drive fails? Replace it, RAID will rebuild
2. Controller fails? Replace it, RAID will be intact

My understanding is you can get RAID controllers that keep the configuration on the controller, so the disks are 1:1 duplicates without proprietary information on the disk. This means you can pull it out and put it into another PC.

I don't see how this would be any more "failure prone" than a disk duplicator. With a disk duplicator:

1. Hard drive fails? Replace it, disk will duplicate later
2. Duplicator fails? Replace it, disk data will be intact

What happens when your primary hard drive you are duplicating gets a bad sector, and when you are duplicating the duplicator can't read it and writes 0's to your other hard drives? With RAID you would be warned and while the data would be lost on one disk it is still intact on the others.

The LSI MegaRaid will probably give you better performance, but that's most noticeable when you do something like RAID-5 where parity calculations are involved. The other benefit of hardware RAID is that if it's battery-backed you're in solid shape in the event of a power failure (data flushed to the controller will be preserved by the battery).
The downside as you've mentioned is that when dealing with hardware RAID controllers if the controller gets blown up you may have difficulty recovering the data (how exact a match you need in terms of hardware depends on the controller/firmware/etc.).

Software RAID-1 is pretty good these days, and if you're just using the machine for a file dump performance will probably be more than adequate. Depending on how the software RAID works you may be able to just throw the disks into another machine and use them (some software like FreeBSD's gmirror stores the RAID info at the end of the drive, so up until that point it's just a regular old disk -- I'm not sure about Windows software RAID but someone should be along soon who can speak with some authority on that).
I would not waste your time and effort on software RAID 5 (sounds like you're not planning to anyway :).

Also standard boilerplate -- as joeqwerty mentioned, you still need a backup -- RAID is a redundancy that protects you if one of your drives dies, but it does nothing to save you if both drives are damaged or you accidentally delete a file that you needed.