The main online brokerages that I use are TD Ameritrade and E*TRADE. I actually had both an original Waterhouse account and an original Ameritrade account before their merger. For all intents and purposes, however, TD Ameritrade is still really two separate brokerages. I will give my opinion of each broker.
Each account that I have has its pluses and minuses. I still prefer to use my original Waterhouse account for most trades. There are some features that Waterhouse still offers that Ameritrade does not. These are access to IPOs, and a better selection of cash sweep accounts. In fact, I got my recent shares in the Bare Escentuals IPO (Nasdaq: BARE) from Waterhouse. However, as far as I know, you can no longer apply for a new Waterhouse brokerage account.
I think that E*TRADE has a better website overall than either Ameritrade or Waterhouse. However, their customer service is not as good. The E*TRADE site doesn't have a tear away "snap ticker" like either Ameritrade or Waterhouse. This makes it harder to look at real time quotes from the main website. The E*TRADE website also provides access to IPOs, and has a decent streamer (for streaming real-time quotes).
Comparing Ameritrade to E*TRADE, I think that Ameritrade has a better streamer. One annoyance that I have found is that Ameritrade doesn't keep track of your capital gains and losses. They say that "the calculation of gains and losses the responsibility of the taxpayer, so TD AMERITRADE does not provide this information." The truth is that I don't rely on this information to calculate taxes, but it is nice to be able to see it to quickly gauge my gains for the year.
As far as commissions are concerned, Ameritrade and Waterhouse are generally a little bit cheaper than E*TRADE. However, I stopped paying attention to commissions when they dropped below $20 per trade. The difference of few dollars is not a big deal.
All three brokerages have access to research such as Standard & Poors (S&P) and Morningstar stock reports. I do use S&P stock reports extensively to do some of my initial research when selecting new stocks to buy.