SHA-256 for sure, it was the first and bitcoin is has biggest marketplace in cryptocurrency
2nd is scrypt and followed by X11/X13 and many more
No. Bitcoin isn't an alt. He was asking about alts. Scrypt is still the most popular alt algo.
Ohh sorry, i though he ask for overall cryptocurrency
![Cheesy](https://bitcointalk.org/Smileys/default/cheesy.gif)
With bitcoin out of list, I think scrypt is the most popular altcoin
Although X13 / X15 getting more popular recently
![Grin](https://bitcointalk.org/Smileys/default/grin.gif)