Do you have any recommendations or tips on the exchanges you ended up using? I've been sending everything to Cryptsy so far though will also do some research to see if there are some better options for particular coins. It seems to be something of a minefield when it comes to dealing with exchanges. I recently had a bad experience with CoinEX, though luckily it all worked out in the end after much chasing.
Also, out of curiosity - what approach is everyone else taking to when to trade the coins mined here on TradeMyBit. Are you sending them out regularly (eg: every 1 or so coins) for sale at the market rate or are you waiting to stockpile a few and then waiting for the best time to trade?
Coin selection was the biggest factor, but exchange rates and Cryptsy's handling of coins was also a factor. It took Cryptsy about 20 hours to post my ALF and NET deposits. Cryptsy is extremely buggy, expensive, and I really hate it, but I like the auto-trading and selection.
In the end, I went with Coins-E for ALF (ALP), NET, ELP, and ELC. Cryptsy for everything else.
As for payout, I looked at total withdrawal fees. My rule was that I didn't want withdrawal fees to exceed 0.1% of the total withdrawal in most cases. I made some exceptions (like DMD). Also, I set a secondary rule that I need at least .005 BTC in value for each coin before I withdraw the coins. For some coins, I set this minimum to about .015. My thought is that you can always manually payout at the end of the day if you want, so it's okay to set the minimums to higher than you think they need to be. Below are my minimums, but these will definitely change over time. After all, I have only been mining here for a day. Some of them, I have never mined, so I don't know how they will "react". Also, I generally mine at 6-7MH/s so you may want lower or higher payouts than these depending on how fast you mine the coins.
ALF = 100
CRC =35
DMD=1
ELC=10
ELP-200
EMD=50
FRK=2
GLX=30
HBN=5
JKC=100
LOT=10000
MEM=600
NET=500
NRB=30
At the end of the day, I check statistics and see if there are any coins that I should manually cash out.
Merc said he wanted to set minimums, but since everyone has different hashing rates, I personally think that the requirement could be number of withdrawals per day. Most of my coins will have only 1 withdrawal per day (or less), but if we mined the exact same coin all day, that coin could have up to 5 or 6 withdrawals at most.