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I think the 3 that are interesting to me the most are bitcoin, ether, and bitshares. And I know that as of late the trend has been away from cpu/gpu based mining, I'm wondering if I can mine ether/bitshares without a dedicated stand alone miner.

Skrt,
Anchorage,AK

Yeah you can still mine ether with GPU/CPU's and there are no Asics for it but plans are that it will turn POS at some point.

Do you know a miner program that will work for different currencies that works on windows/linux ?

Skrt
Anchorage,AK

Not for different ones no. Most of the coins I am interested in lately are Proof-of-Stake (BTS/STEEM).

Ethereum and Zcash are the only ones that are still mine-able and that I have had an interest in. Were you able to find any miners on that bitcointalk link I provided? (haven't been actively mining ever since my last GPU got burnt)