By ship
A more expensive and more time consuming option from Phnom Penh $35, 6 hr or Battambang US$20-25, 5 hr is to take a Soviet style Hydrofoil across the Tonle Sap lake. These can be fantastic trips giving you the opportunity to view life on the lake, floating houses, working fishermen, and to get a sun-tan if you choose to sit on the roof of the boat. However, the trip can be ruined due to bad weather. Remember to use sunscreen and take a waterproof jacket. You will not be always able to access your luggage during the journey sometimes the baggage is available, sometimes it is not. If you have the time, it is better to visit the floating villages as day trips from Siem Reap than to see them from the boat.
By road
Many companies, including Phnom Penh Sorya Transport (http://www.ppsoryatransport.com/ Capitol Tours, and GST Express) operate bus services to/from Siem Reap. Direct buses go to Phnom Penh US$10, Pakse US$30, Don Det in the 4,000 Islands region of Laos US$27, Kampong Cham, Soung, Battambang, and Kor Kong. Advance bookings are advisable, and can also be sorted out by most travel agents and guesthouses for a US$1-2 fee. Buses generally leave between 7AM-3PM but there is a night bus as well if you want to not spend the daytime travelling which leaves at midnight.
From Thailand, the nearest border crossings are at Aranyaprathet/Poipet, 3 hr to the north, and Hat Lek/Koh Kong on the coast. See those articles for information on how to get to and cross the border. As a result of recent road pavings, the roads from these border crossings to Siem Reap are in excellent condition. From Poipet, you can take a taxi US$25 minimum, 2-3 hr, max 4 passengers or an overcrowded bus US$10, 3 hr, leaves when full, not as comfortable.
The best budget option is to catch a Thai government bus to the border at Poi Pet don't buy from Khao San Road, buy the Cambodian visa directly for US$20, then after being stamped into the country find yourself a group of four to catch a reasonably comfortable taxi to Siem Reap US$25-30. This will get you to Siem Reap on time, in comparable comfort without funding scammers. While you are processing your papers at the border beware of extra friendly government employees who offer to help you. Some of them may try and take you by bus to a taxi stand where you will pay too much to exchange money at the "government" exchange booth. Then, they may try to make you pay up to double the going rate for taxis to Siem Reap US$10 per person, instead of US$5.
Alternatively, you could join the backpacking masses and pay 200-600 baht for an uncomfortable bus ride directly from Khao San Road. Buses leave Khao San Road around 8AM and arrive in Siem Reap any time between 5PM-3AM, a reasonable price would be 450 baht. The trip length does not really depend on road conditions but on the mood of the driver. Because he gets a commission if you stay at the guesthouse at which he drops you off, he will try to arrive there as late as possible because if you are tired and afraid of walking around in Siem Reap late at night, you are more likely to stay at that guesthouse. Note that there is no obligation to stay at such guesthouse, regardless of what the guesthouse owners tell you. Even if you start in Bangkok on a big aircon bus, you will almost certainly have to switch to the back of a pickup or stuffed minibus at the Cambodian border. The bus operators and others will assure you that you're better off paying 1,000 baht US$30 or even more for the visa - which should cost US$20. The driver and/or the person that will make your 'fast' visa can get offended if you don't believe their lie: you cannot do the visa by yourself. Stand your ground and join the line at the border - the bus won't leave without you, because the driver wants the guesthouse commission you represent. As an alternative, you can always walk from the bus stop to the Thai border exit - just keep aware of your surroundings to avoid being pickpocketed or inadvertently walking into a fake border crossing. Custom officers will be likely to ask you more than the official price too 800 baht/US$26, or extra services like filling out a form for you for 50 baht to avoid you some hassle there won´t be any, you just fill the form later in the stamping section.