In this paper we report on dye structure–optical property correlations for a range of near-infrared emitting (NIR, 650–900 nm) fluorescent dyes in a 9–14 nm diameter core-shell silica particle architecture (C dots), including Cy5, Alexa Fluor 700, DY730, Alexa Fluor 750, and DY780. For each dye an apparent per-dye enhancement in fluorescence is observed over free dye in aqueous solution ranging from 1.2× to 6.6×, highlighting the versatility of the silica encapsulation approach. For the Cy5 and DY730 dye/particle sample pairs photobleaching was undertaken and revealed that the particles photobleach slower than the dyes. For a particular NIR dye series with identical chemical backbone, DY730, DY731, DY732, and DY734, we demonstrate that with increasing number of sulfonated substituent groups the per-dye brightness enhancement decreases. Finally, we show that in special cases, like Cy5, brightness enhancement of dyes in dots over free dye may be a combination of effects from dye conjugation chemistry and immobilization in the silica matrix. These results provide powerful design criteria for next generation optical probes for applications ranging from bioimaging to security.