It depends what you're planning to do. If you're working with analog electronics, then you probably won't need the digital channels. As most people end up playing with embedded systems at some point though, the digital channels become pretty useful.
The digital channels on the MSO scopes are typically higher performance sampling than the standalone sniffers. This can be essential if you start working with high speed digital, FPGAs etc. Having said that, for playing with general embedded stuff, you aren't likely to need that. And the standalone units generally have excellent software, which can decode lots of protocols for no more money, as opposed to the upgrade approach on mixed signal scopes.
As well as being higher speed, capturing the signal on a scope also has the advantage that the signals will be correlated in time with your analog signals, which can be extremely useful for mixed signal systems.
As for waveforms per second, it's nice, but I wouldn't get hung up on it as the deciding factor, whereas factors like memory depth is absolutely critical for long single shot captures, the need for which comes up extremely frequently