As far I can tell, current "real" projects are (roughly by date of conception).

* Bitcoin
* NXT
* Cryptonote (now Monero)
* BitShares (now Steemit)
* Ethereum
* Sia
* Iota
* Waves (reimplementation of NXT to be more ETH-like)
* Cardano
* Tezos

(i'm sure i've missed something, please tell if you know about others)

By real I consider complete and often highly innovative codebase from scratch, not just copying and bending previous stuff, nor piggybacking on existing networks (tokens).

Vast majority of alts out there is just bitcoin slightly tweaked.

Honorable mentions, as those are not satoshian BFT blockchains, but interesting nevertheless in their own right:
* Ripple
* Storj (modern seti@home for spare disk space)
* Byteball (TX DAG)
* Hyperledger ("Consensus" of non-deterministic contracts)
* Many chains like zcash or dash, though highly divergent, are still ultimately rooted in the bitcoin codebase

As for how to deal with the clones, those are not necessarily a scam, often it makes sense to just copy the base and slightly tweak it. Bitcoin had many influental forks (such as Litecoin, Peercoin or Blackcoin) and to a lesser degree NXT.

edit: added more OC implementations