I use GoldWave. It suits my needs.

For those that can't get their bootsound to work, remember that you want a sound that is equal to or less than the size of the original boot sound. If the uncompressed WAV file is too large, ATRAC3 is actually rather effective in compressing it without losing too much quality. If the highest quality AT3 compression doesn't make it small enough, though, you'll have to use a lower quality, which might sound like poo poo.

I don't know how well S_king's utility works, though, because I manually inserted my ATRAC3 compressed wav using Hex Workshop, and it worked. So I've had no need for it, really.

It's nice not having to use .vag format, though. MFAudio likes to crash on me at random -.-