In the San Francisco Bay Area, these are the free resources for getting a thorough STD check-up.  Every place in the US (and most of the world) has similar resources.

STDtest.org
online testing
24 hours/7 days a week

SF City Clinic (STD Clinic)
356 7th Street
415.487.5500

Testing:
Monday, Wednesday, Friday 8am to 4pm
Tuesday 1pm to 6pm
Thursday 1pm to 4pm

Magnet (This place is cool, except for a grumpy receptionist)
4122 18th Street

Testing:
Wednesday - Friday 4pm to 8pm
Saturday 1pm to 5pm

Positive Health Programs West
3180 18th Street, Suite 301
Monday - Friday 10am to 2:30pm

Castro Mission Health Center
1350 17th Street
415.487.7500
Also home to Dimensions (queer youth clinic)

Cole Street Youth Clinic
555 Cole Street
415.751.8181

Haight Ashbury Free Medical Clinic
558 Clayton Street
415.487.5632

Mission Neighborhood Health Center
240 Shotwell Street
415.552.3870

Tom Waddell Clinic (awesome place that works with homeless and poor people)
50 Ivy Street
415.554.2950

Want a provider who is gay or gay friendly?
The Gay and Lesbian Medical Association (GLMA) has a list of gay providers in the Bay area.  Call 415.255.4547 for more information.