Pat CJ and Cody can advise you much more thoroughly than I, but these are some of my favorite cultivars of emergent and submergent macrophytes:
Submergent
American Pondweed - fairly easily managed and can fish through it easily.
Illinois Pondweed - pretty similar I think I have both species present - both seem to appear later in the season for me.
Eelgrass - Spiral and corkscrew [maybe the same thing?]I don't have it, but I want it. A favorite of Cody and CJs.
Bushy type Pondweed - Various pondweeds like Sago, Horned, etc. can be good but my Baby pondweed is starting to become a management issue. Can be easily treated, and one can always opt for an organic solution with GC stocking. I bumped my population to 3/acre to help manage the Baby Pondweed last Summer.
Hybrid Lillies - Cody is an expert on lillies - has written extensively on the subject and suggests several good cultivars that are easy to manage and bloom in various colors. I want to try to establish them in my upper ponds that lack GC.
Emergent
Cattails to an extent can help utilize excess nutrients - a thin line of them along Northern banks exposed to lots of wave action can be a great natural defense. One will have to treat them annually to keep the colony managed - don't let them get away from you. Bear in mind cattails are a preferred forage item for muskrats - so I eradicate mine several times annually - can't afford the muskrat factor.
Various sedges and rushes are great emergent vegetation. I can't ID my species, but I have some growing naturally in few places on the main pond. I'll be transplanting it throughout the main pond this year in addition to the upper ponds and hopefully it propagates.
Arrowhead is a cool plant, and that also occurred for me naturally. Drawback is that I think Skrats also love grazing it...but I don't have the heart to treat it. It's a late season comer at my ponds - shows up around mid to late July.
Tons of other candidates I'm missing certainly, but these are the ones with which I'm familiar and have managed to an extent. Rooted vegetation should appear naturally - but some specialty species like Lillies and eelgrass may need to be introduced.
Bill has forgotten more than I know...he'll be along shortly. Try a Google search for "eelgrass pondboss" and "hybrid lillies pondboss" and start printing/highlighting.
Aren't we lucky to have those resources in our family?