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You can setup your affiliate program by signing up for affiliate network or by purchasing your own affiliate tracking software.
Affiliate networks track affiliates, handle sending out the checks to affiliates, provide other necessary support both to affiliates and merchants, including affiliate fraud management.
Additionally, you will have access to a base of potential affiliates that often have more confidence in third party monitoring.
First three listed are the biggest affiliate networks for well established businesses.

BeFree Their tracking system are used by dozens of well known merchants. However for affiliates many of these merchants are better known for their fraudulent activity.
Set up fee: around $6000.
Initial (escrow) deposit: n/a.
Transaction fee: 2-3% with a minimum charge of $3000 monthly.

Commission Junction The largest and very friendly network both for affiliates and merchants. Excellent reporting. Very attractive feature for affiliates is that commissions earned from all merchants are pooled together in one check.
Set up fee: $2250 and $250 yearly fee.
Initial deposit: $3000.
Transaction fee: 30% or $0.30 with a minimum charge of $500 monthly.
Recommended.

LinkShare Another major affiliate network. Became more attractive for affiliates, because now requires merchants to pay no later than 35 after the end-of-month.
Set up fee: $10,000 and $2000 yearly fee.
Initial deposit: n/a.
Transaction fee: 2-3% with a minimum charge of $2000 monthly.

Below are listed smaller and more affordable affiliate networks for smaller merchants.

Affiliate Fuel Does not run any rev-share (pay-per-sale) campaigns. In addition to pay-per-lead campaigns, also delivers CPM direct email, newsletter and CPC campaigns.
Set up fee: Free.
Initial deposit: $2500 minimum. All undelivered funds in an advertiser's account will be fully refundable.
Transaction fee: 30%.

ClickBank Credit card processing company and affiliate network with several thousands of merchants selling info-products.
Set up fee: $49.95.
Initial deposit: n/a.
Transaction fee: $1 + 7.5% fee per sale.

ClickXchange Large pool of cheap merchants.
Set up fee: Free.
Initial deposit: $500.
Transaction fee: 30% with a minimum charge of $42 monthly.

clixGalore Reliable affiliate network comprising of over 1000+ merchants and ten of thousands of affiliates across their three networks in the USA, UK and Australia. CPA and CPC models.
You may operate your affiliate program in either United States dollars, Australian dollars, British Pounds or Euro.
Offers 4 scaled levels of affiliate marketing services to the merchants.
Set up fee: Free.
Initial deposit: From $75 to $250.
Transaction fee: 25% .
Recommended.

Direct Response Solid company supporting both CPA and CPC programs.
If you choose to add a campaign on a CPA basis (DirectLeads), you are committing to a minimum purchase of $1000, non transferable and non-refundable, with a minimum effective cost per click (CPC) of $.05.
For CPC campaign (DirectClicks), minimum investment to get started is $250.00. Cost per click hover from $0.08 to $0.20, depending on the number of clicks you purchase.

FineClicks Quality affiliate network, recently acquired by ShareSale. Various offer types: pay per lead, pay per sale, pay per click, and CPM popup/under.
Set up fee: Free.
Initial deposit: $350.
Transaction fee: 20-30% (35% for CPC campaigns). Minimum transaction $0.07.
Recommended.

LeadCrunch Small CPA network with good reputation. To get information about their solutions for merchants you should contact them.

Leadhound Medium size network paying only via PayPal therefore not available for many international affiliates.
Set up fee: $149.
Initial deposit: $200.
Transaction fee: 30%.

ShareASale Top quality low-cost affiliate network offering outstanding support. Tracks pay-per-sale, pay-per-lead, and pay-per-click affiliate programs.
Set up fee: $150.
Initial deposit: $50.
Transaction fee: 20%.
Recommended.

TradeDoubler The largest European affiliate network. Operates in Austria, Denmark, Finland, France, Germany, Ireland, Italy, Netherlands, Norway, Spain, and U.K. Each country office is operated as a TradeDoubler subsidiary with its own website and affiliate network.
Prices can vary depending upon your requirements.
Set up fee: £900 for the traffic program and up to £2900 for the public affiliate program.
Initial deposit: n/a.
Transaction fee: £215 per month.
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