This patch comes from OpenSSL upstream code, and the change has been commited to OpenSSL 1.0.2.
  http://git.openssl.org/gitweb/?p=openssl.git;a=commit;h=fbd2164044f92383955a801ad1b2857d71e83f27
  http://git.openssl.org/gitweb/?p=openssl.git;a=commit;h=51e7a4378a78bb0870a2cdc5c524c230c929ebcb
  http://git.openssl.org/gitweb/?p=openssl.git;a=commit;h=2dabd822366df7b2608b55d5ca5f31d5d484cbaf

Index: openssl/crypto/x509/x509_trs.c
============================================================================
$ diff -ru crypto/x509/x509_trs.c crypto/x509/x509_trs.c 
--- openssl/crypto/x509/x509_trs.c.orig    4 Dec 2012 17:26:04 -0000    1.133.2.11.2.6.2.3
+++ openssl/crypto/x509/x509_trs.c    14 Dec 2012 14:30:45 -0000    1.133.2.11.2.6.2.4
@@ -119,6 +119,14 @@ int X509_check_trust(X509 *x, int id, int flags)
     int idx;
     if (id == -1)
         return 1;
+    /* We get this as a default value */
+    if (id == 0) {
+        int rv;
+        rv = obj_trust(NID_anyExtendedKeyUsage, x, 0);
+        if (rv != X509_TRUST_UNTRUSTED)
+            return rv;
+        return trust_compat(NULL, x, 0);
+    }
     idx = X509_TRUST_get_by_id(id);
     if (idx == -1)
         return default_trust(id, x, flags);
Index: openssl/crypto/x509/x509_vfy.c
============================================================================
$ cvs diff -u -r1.105.2.9.2.4.2.3 -r1.105.2.9.2.4.2.4 x509_vfy.c
--- openssl/crypto/x509/x509_vfy.c    14 Dec 2012 12:53:48 -0000    1.105.2.9.2.4.2.3
+++ openssl/crypto/x509/x509_vfy.c    14 Dec 2012 14:30:46 -0000    1.105.2.9.2.4.2.4
@@ -149,6 +149,33 @@
 }
 #endif
 
+/* Given a certificate try and find an exact match in the store */
+
+static X509 *lookup_cert_match(X509_STORE_CTX *ctx, X509 *x)
+    {
+    STACK_OF(X509) *certs;
+    X509 *xtmp = NULL;
+    int i;
+    /* Lookup all certs with matching subject name */
+    certs = ctx->lookup_certs(ctx, X509_get_subject_name(x));
+    if (certs == NULL)
+        return NULL;
+    /* Look for exact match */
+    for (i = 0; i < sk_X509_num(certs); i++)
+        {
+        xtmp = sk_X509_value(certs, i);
+        if (!X509_cmp(xtmp, x))
+            break;
+        }
+    if (i < sk_X509_num(certs))
+        CRYPTO_add(&xtmp->references,1,CRYPTO_LOCK_X509);
+    else
+        xtmp = NULL;
+    sk_X509_pop_free(certs, X509_free);
+    return xtmp;
+    }
+
+
 int X509_verify_cert(X509_STORE_CTX *ctx)
 {
     X509 *x, *xtmp, *chain_ss = NULL;
@@ -304,8 +331,17 @@ int X509_verify_cert(X509_STORE_CTX *ctx)
 
     /* we now have our chain, lets check it... */
 
-    /* Is last certificate looked up self signed? */
-    if (!ctx->check_issued(ctx, x, x)) {
+    i = check_trust(ctx);
+
+    /* If explicitly rejected error */
+    if (i == X509_TRUST_REJECTED)
+        goto end;
+    /*
+     * If not explicitly trusted then indicate error unless it's a single
+     * self signed certificate in which case we've indicated an error already
+     * and set bad_chain == 1
+     */
+    if (i != X509_TRUST_TRUSTED && !bad_chain) {
         if ((chain_ss == NULL) || !ctx->check_issued(ctx, x, chain_ss)) {
             if (ctx->last_untrusted >= num)
                 ctx->error = X509_V_ERR_UNABLE_TO_GET_ISSUER_CERT_LOCALLY;
@@ -340,14 +376,6 @@ int X509_verify_cert(X509_STORE_CTX *ctx)
     ok = check_name_constraints(ctx);
 
     if (!ok)
-        goto end;
-
-    /* The chain extensions are OK: check trust */
-
-    if (param->trust > 0)
-        ok = check_trust(ctx);
-
-    if (!ok)
         goto end;
 
     /* We may as well copy down any DSA parameters that are required */
@@ -630,28 +658,53 @@ static int check_name_constraints(X509_STORE_CTX *ctx)
 
 static int check_trust(X509_STORE_CTX *ctx)
 {
-#ifdef OPENSSL_NO_CHAIN_VERIFY
-    return 1;
-#else
     int i, ok;
-    X509 *x;
+    X509 *x = NULL;
     int (*cb) (int xok, X509_STORE_CTX *xctx);
     cb = ctx->verify_cb;
-/* For now just check the last certificate in the chain */
-    i = sk_X509_num(ctx->chain) - 1;
-    x = sk_X509_value(ctx->chain, i);
-    ok = X509_check_trust(x, ctx->param->trust, 0);
-    if (ok == X509_TRUST_TRUSTED)
-        return 1;
-    ctx->error_depth = i;
-    ctx->current_cert = x;
-    if (ok == X509_TRUST_REJECTED)
-        ctx->error = X509_V_ERR_CERT_REJECTED;
-    else
-        ctx->error = X509_V_ERR_CERT_UNTRUSTED;
-    ok = cb(0, ctx);
-    return ok;
-#endif
+    /* Check all trusted certificates in chain */
+    for (i = ctx->last_untrusted; i < sk_X509_num(ctx->chain); i++) {
+        x = sk_X509_value(ctx->chain, i);
+        ok = X509_check_trust(x, ctx->param->trust, 0);
+        /* If explicitly trusted return trusted */
+        if (ok == X509_TRUST_TRUSTED)
+            return X509_TRUST_TRUSTED;
+        /*
+         * If explicitly rejected notify callback and reject if not
+         * overridden.
+         */
+        if (ok == X509_TRUST_REJECTED) {
+            ctx->error_depth = i;
+            ctx->current_cert = x;
+            ctx->error = X509_V_ERR_CERT_REJECTED;
+            ok = cb(0, ctx);
+            if (!ok)
+                return X509_TRUST_REJECTED;
+        }
+    }
+    /*
+     * If we accept partial chains and have at least one trusted certificate
+     * return success.
+     */
+    if (ctx->param->flags & X509_V_FLAG_PARTIAL_CHAIN) {
+        X509 *mx;
+        if (ctx->last_untrusted < sk_X509_num(ctx->chain))
+            return X509_TRUST_TRUSTED;
+        x = sk_X509_value(ctx->chain, 0);
+        mx = lookup_cert_match(ctx, x);
+        if (mx) {
+            (void)sk_X509_set(ctx->chain, 0, mx);
+            X509_free(x);
+            ctx->last_untrusted = 0;
+            return X509_TRUST_TRUSTED;
+        }
+    }
+
+    /*
+     * If no trusted certs in chain at all return untrusted and allow
+     * standard (no issuer cert) etc errors to be indicated.
+     */
+    return X509_TRUST_UNTRUSTED;
 }
 
 static int check_revocation(X509_STORE_CTX *ctx)
@@ -1526,6 +1579,8 @@ static int internal_verify(X509_STORE_CTX *ctx)
     if (ctx->check_issued(ctx, xi, xi))
         xs = xi;
     else {
+        if (ctx->param->flags & X509_V_FLAG_PARTIAL_CHAIN && n == 0)
+            return check_cert_time(ctx, xi);
         if (n <= 0) {
             ctx->error = X509_V_ERR_UNABLE_TO_VERIFY_LEAF_SIGNATURE;
             ctx->current_cert = xi;
Index: openssl/crypto/x509/x509_vfy.h
============================================================================
$ cvs diff -u -r1.67.2.3.4.1 -r1.67.2.3.4.2 x509_vfy.h
--- openssl/crypto/x509/x509_vfy.h    26 Sep 2012 13:50:42 -0000    1.67.2.3.4.1
+++ openssl/crypto/x509/x509_vfy.h    14 Dec 2012 14:30:46 -0000    1.67.2.3.4.2
@@ -406,6 +406,9 @@
 /* Check selfsigned CA signature */
 # define X509_V_FLAG_CHECK_SS_SIGNATURE          0x4000
 
+/* Allow partial chains if at least one certificate is in trusted store */
+# define X509_V_FLAG_PARTIAL_CHAIN               0x80000
+
 # define X509_VP_FLAG_DEFAULT                    0x1
 # define X509_VP_FLAG_OVERWRITE                  0x2
 # define X509_VP_FLAG_RESET_FLAGS                0x4
Index: openssl/apps/apps.c
============================================================================
$ cvs diff -u -r1.133.2.11.2.6.2.3 -r1.133.2.11.2.6.2.4 apps.c
--- openssl/apps/apps.c    4 Dec 2012 17:26:04 -0000    1.133.2.11.2.6.2.3
+++ openssl/apps/apps.c    14 Dec 2012 14:30:45 -0000    1.133.2.11.2.6.2.4
@@ -2238,6 +2238,8 @@
         flags |= X509_V_FLAG_NOTIFY_POLICY;
     else if (!strcmp(arg, "-check_ss_sig"))
         flags |= X509_V_FLAG_CHECK_SS_SIGNATURE;
+    else if (!strcmp(arg, "-partial_chain"))
+        flags |= X509_V_FLAG_PARTIAL_CHAIN;
     else
         return 0;