I choose controllers for Mega Man-style game, but for CV series I always prefer keyboard control on emulator.
For Castlevania Chronicles (PS1), since there's only several basic moves during gameplay, up, down, left, right, jump, attack, it's natural that I padded my button mapping to: W,A,S,D for directions, K for attack and L for jump, and I keep using keyboards for almost 3 years on the emulator until I acknowledged a Japanese PSN version that has differences compared to all the versions I've beaten dozen times at around 2012.
But for Harmony of Dissonance, I prefer PC controllers because of the power of L/R dashing is SO addictive. And the hacked version (Revenge of the Findesiecle) just rocks and it boosts almost all the possibility of Harmony of Dissonance engine, thus became a personal reason that I must play the hacked version instead of regular version and must be on the PC when I want to pick Harmony of Dissonance again. AND THE HACKED VERSION IS STILL IN THE UPDATE PROGRESS NOW. I gave the 2012 revision of the hack 10/10 rank (The newer updated version released in this year is not that awesome for me, thanks to the graphic glitch)
In last few months I got two Wii classic controllers (One is a 3rd party bootleg but I just don't care), two PS1 controllers with analog joysticks and one without, two SNES-style 3rd party controllers, and other things in weird shape. Now I feel the analog joysticks on the controller are always jamming with my fingers when I thrown myself into serious CV-style games on PC, and I had a second thought about the controllers with joysticks.
Other thing is, when I plugged the Wii classic controller to the PC (Using some external hardware device, of course) some games don't even let you control the characters with d-pad, but with JOYSTICKS instead. Castlevania: The Lecarde Chronicles and Rosenkreuzstilette suffered from this, both are doujin/fan-made/independent works, both are on the PC, and both have the game style I can put 100% of my love power inside, and I'm so sad. Then I started to worry a LOT about controllers in video gaming.