Inclusion Criteria:

1. Patients must have histologically or cytologically confirmed Stage IV or recurrent or unresectable Stage III melanoma of non-choroidal origin. Patients must have easily accessible tumor for biopsy (in treating physician's or PI's opinion). A patient does not need easily accessible tumor for biopsy only if: - patient had tumor sample collection within 3 months prior to registration; - tumor sample was collected appropriately (snap frozen or OCT-embedded); and - patient agrees to provide these tumor samples for analysis planned in this trial
2. Patients must have measurable disease, defined as at least one lesion that can be accurately measured in at least one dimension (longest diameter to be recorded) as >/= 20 mm with conventional techniques or as >/= 10 mm with spiral CT scan. In case of obviously visible cutaneous metastatic lesions, the margins of the lesions should be clearly defined and measured in at least one dimension as >/= 10 mm.
3. Phase I study: There is no limitation on the number of prior therapeutic regimens.
4. Phase II study: Patients may have received up to 1 systemic chemotherapy regimen for metastatic melanoma: No limit in number of prior biological or immunotherapy: No limit for the number of regional chemotherapy regimens unless all target lesions are located w/in the prior regional treatment field. If all target lesions are located w/in the prior regional treatment field, only up to one prior regional chemotherapy regimen is allowed. If pts received prior chemotherapy for other cancers, no limit in number of prior chemotherapy regimens as long as the last chemotherapy was at least 5 years ago.
5. Age 18 years or older. Because no dosing or adverse event data are currently available on the use of BAY43-9006 in combination with CCI-779 in patients <18 years of age, children are excluded from this study, but will be eligible for future pediatric phase 1 combination trials.
6. ECOG performance status less than or equal to 1.
7. Patients must have normal organ and marrow function as defined as: leukocytes >/= 3,000/mcL; absolute neutrophil count >/= 1,500/mcL; platelets >/= 100,000/mcL; fasting serum cholesterol </= 350 mg/dL; fasting triglycerides </= 400 mg/dL; total bilirubin within normal institutional limits; ALT/AST </= 2.5 X institutional upper limits of normal; creatinine within normal institutional limits or creatinine clearance >/= 60 ml/min/1.73 meter squared for patients with creatinine levels above institutional normal.
8. Patients on prophylactic anticoagulation therapy (e.g., low-dose warfarin) are eligible provided their coagulation parameter levels are as follows: Prothrombin time (INR; International Normalized Ratio of prothrombin time) <1.1 x institutional upper limit of normal.
9. Eligibility of patients receiving any other medications or substances known to affect or with the potential to affect the activity or pharmacokinetics of BAY43-9006 or CCI-779 will be determined following review of individual cases by the Principal Investigator. Patients cannot be receiving enzyme-inducing antiepileptic drugs (EIAEDs) such as phenytoin, carbamazepine, phenobarbital, rifampin, or St. John's wort.
10. The effects of BAY43-9006 and CCI-779 on the developing human fetus are unknown. For this reason and because other tyrosine kinase inhibitors and mRNA translation inhibitors are known to be teratogenic, women of child-bearing potential and men must agree to use adequate contraception (hormonal or barrier method of birth control; abstinence) prior to study entry and for the duration of study participation. Should a woman become pregnant or suspect she is pregnant while participating in this study, she should inform her treating physician immediately.
11. Ability to understand and the willingness to sign a written informed consent document.

Exclusion Criteria:

1. Patients who have had chemotherapy or radiotherapy within 4 weeks (6 weeks for nitrosoureas or mitomycin C) prior to entering the study or those who have not recovered to grade 1 toxicity (except for peripheral neuropathy, for which </= grade 2 toxicity is allowed to participate) from adverse events due to agents administered more than 4 weeks earlier.
2. For phase II study portion, patients may not have previously received either BAY43-9006 or CCI-779 or any other agents targeting raf, VEGF/VEGFR, or mTOR. However, for phase I study portion, this exclusion criterion does not apply.
3. Patients may not be receiving any investigational agents other than BAY43-9006 and CCI-779.
4. Patients with known brain metastases are excluded because of their poor prognosis and because they often develop progressive neurologic dysfunction that would confound evaluation of neurologic and other adverse events. The following exception is allowed: patients without radiographical evidence of recurrence in the brain for >/= 3 months after complete resection of brain metastases or who have asymptomatic brain metastases stable for >/= 3 months since whole brain radiation therapy and/or stereotactic radiosurgery are eligible. Patients must not require steroid treatment for brain metastases.
5. History of allergic reactions attributed to compounds of similar chemical or biologic composition to BAY43-9006 or CCI-779.
6. Uncontrolled hypertension with systolic blood pressure of > 140 mmHg on 2 separate days within 1 week before enrollment or diastolic pressure > 90 mmHg on 2 separate days within 1 week before enrollment. However, patients with well-controlled hypertension are eligible.
7. Patients must not have any evidence of bleeding diathesis or coagulopathy.
8. Patients on full-dose anticoagulation (i.e. warfarin, IV heparin, low-molecular weight heparin).
9. Patients with any condition (e.g., gastrointestinal tract disease resulting in an inability to take oral medication or a requirement for IV alimentation, prior surgical procedures affecting absorption, or active peptic ulcer disease) that impairs their ability to swallow pills are excluded.
10. Uncontrolled intercurrent illness including, but not limited to, uncontrolled hypertension, ongoing or active infection, symptomatic congestive heart failure, unstable angina pectoris, cardiac arrhythmia, or psychiatric illness/social situations that would limit compliance with study requirements.
11. Pregnant women are excluded from this study because BAY43-9006 is a serine-threonine kinase inhibitor and CCI-779 is an mRNA translation inhibitor, both of which have the potential for teratogenic or abortifacient effects. Because there is an unknown but potential risk for adverse events in nursing infants secondary to treatment of the mother with BAY43-9006 or CCI-779, breastfeeding should be discontinued if the mother is treated with either of these agents.
12. HIV-positive patients on combination antiretroviral therapy are ineligible because of the potential for pharmacokinetic interactions with BAY43-9006 and/or CCI-779. In addition, these patients are at increased risk of lethal infections when treated with marrow-suppressive therapy. Appropriate studies will be undertaken in patients receiving combination antiretroviral therapy when indicated.
13. Patients undergoing major surgery or a sustaining a significant traumatic injury within 21 days prior to treatment are ineligible.