Jeez, I feel like I'm on my e-mail at work. <g>
Digi has their own standard format for plugs called RTAS (Real Time Audio Suite) and their file based standard AudioSuite. Check Digi's web site if you want a more in depth overview. Every one of the major developers (pretty much) has RTAS versions. Waves, Bomb Factory, Antares, Kind of Loud, Metric Halo all have some pretty cool software. I currently run Waves NPP1 & 2 and find the Ren EQs and Ren Compressor essential (as do most users). Their TrueVerb is decent, but really no software verb will do what a good piece of outboard kit will do. Quite a few people swear by Metric Halo's Channel Strip.
RTAS is, put simply, the native version of the TDM plug-in standard that Digi established on their high end workstations (the platform that stared this whole DAW thing). As such it is pretty much "in for a penny, in a pound". RTAS is currently only supported in ProTools and ProTools doesn't directly any other plug-in format (ie VST). For me that's fine - I'm sold on and committed to ProTools as my tracking and mixing platform. I also like the fact that most commercial studios here in Chicago run full TDM systems and when I need to go to one, my RTAS plugs (with all of the automation I can apply to them) will directly translate to the TDM version. If you're heavily invested in VST stuff, you might want to think your purchase through a little more.
OTOH the 001 does support third party apps (DP, Logic, etc.) through a free plug called Direct Connect (again check Digi's site). Quite a few users choose LAP or DP as their midi app and then route outputs into PT using Direct Connect - this way you can use your VST stuff on midi and enjoy RTAS for audio. A few (very few) use LAP or MotU as their audio and midi platform and just use the 001 as an interface.
BTW - the system does ship with a set of Digi plugs - RTAS and AudioSuite. There's a time compression/expansion plug I use quite a bit on loops and a decent set of delays. There's also a full set of dynamics (real time EQs, compressors, limiters) and and, I think, they're still bundling their verb and a de-esser. It's a pretty respectable set to get started with although most people doing more serious stuff opt for the third party products. I hated the verb, don't really use their dynamics and the de-esser is okay.
I'm heading off to mix and as always, YMMV.
K