I wrote a blog last month on how to set Lead record type in a Web-to-Lead form, you can use hidden field, for example:
<input type=hidden name="recordType" id="recordType" value="01250000000HkoV">
We can use any field, include Lead custom field as hidden field using same format, but you need to change the name with the correct Field Id.
<input type=hidden name="FieldId" value="any value">
<input type=hidden name="00N30000000h9w3" value="From Website">
How to get field id? Go the Setup menu - Customize - Leads - Fields, scroll down and look for the field and click the field name.
For screenshot above, we can easily know the field id for this field is 00N30000000h9w3