I use BTC-E for all my trading of Alt coins. I have never had a problem (knock on wood), with any deposits, trades, or withdrawals. I have done several transactions with BTC, LTC, and NMC, so I can vouch for at least those 3 going smoothly.
The only problem is that it is pretty difficult to get USD onto the website. Each time I have resorted to buying BTC on coinbase.com and then sending it over to BTC-E. The downside of doing that is that you get hit with the 1% fee on coinbase, and then the USD/BTC is usually lower on BTC-E than on coinbase, so you get skimmed a little off the top right there too...
You withdraw fiat from btce?? I've always sent to stamp for that. Which method do you use and how is it like?