You specifically mentioned stock certificates, so I'll leave bond certificates for another time.
Here are a few of my nicer ones.
American Express Co. showing the geometric star cancel frequently misattributed as a postal cancel, certificate signed by Henry Wells and William Fargo of Wells Fargo fame.
Early stock certificate with R36a (CV $500).
Red and green is always a great color combo.
Very scare 25-cent Warehouse Receipt part perforate (R50b, CV = $1,100).
Very unusual, a completely holographic (handwritten) stock certificate.